Alignments for a candidate for putA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Burkholderia phytofirmans PsJN

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate BPHYT_RS19355 BPHYT_RS19355 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>FitnessBrowser__BFirm:BPHYT_RS19355
          Length = 1309

 Score = 1751 bits (4534), Expect = 0.0
 Identities = 916/1339 (68%), Positives = 1054/1339 (78%), Gaps = 36/1339 (2%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RLK  A  ++RTPHWLIKQAIF YLE++E G +P E S   TGS
Sbjct: 1    MASTTLGVKVDDLLRSRLKDAATRLERTPHWLIKQAIFAYLEKIEHGQLPPELSGV-TGS 59

Query: 61   EGAADGADAFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQARL 120
               ADGA        DGA  PFLEFAQ+VQPQSVLRAAITAAYRRPE EC+P L+ QARL
Sbjct: 60   ADLADGASVEQ--EEDGASHPFLEFAQNVQPQSVLRAAITAAYRRPEPECLPFLVGQARL 117

Query: 121  PHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRIP 180
            P   A     MA  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEALLRIP
Sbjct: 118  PANLAGDVQTMAGKLVETLRTKSKGGG----VEGLIHEFSLSSQEGVALMCLAEALLRIP 173

Query: 181  DKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRII 240
            D+ATRDALIRDKIS  +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E  LS ALTR+I
Sbjct: 174  DRATRDALIRDKISKGDWKSHMGQAPSMFVNAATWGLMITGKLVTTNSETSLSSALTRLI 233

Query: 241  GKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEAD 300
            GKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA TEAD
Sbjct: 234  GKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAATTEAD 293

Query: 301  AQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKSL 360
            AQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALH RYSR+Q ER + EL  R++SL
Sbjct: 294  AQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHARYSRSQQERTMSELLPRVRSL 353

Query: 361  TLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDY 420
             +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PELAGWNGIGFVVQ YQKRCPFVIDY
Sbjct: 354  AILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELAGWNGIGFVVQAYQKRCPFVIDY 413

Query: 421  LIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLSV 480
            +IDLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+KLLS 
Sbjct: 414  IIDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKKLLSA 473

Query: 481  PDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRP 540
            PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V G     K NRP
Sbjct: 474  PDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTG---RDKLNRP 530

Query: 541  CRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEG 600
            CR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+ +++ +L+ADPV    ++     
Sbjct: 531  CRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADENVAIKDLIADPVDEASKI----V 586

Query: 601  ALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAA 660
             LG PH +I  PR LYG  R NS G+DLSNEHRLASLSSALLA       A P+L     
Sbjct: 587  PLGAPHAKIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASAHHPWRAAPMLEDNEI 646

Query: 661  AGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALER 720
            A   V     VRNP+D RD+VG V EA+   V AAL  AV AAPIWQATP D RA  L R
Sbjct: 647  A---VGVARDVRNPADHRDLVGTVVEATPEHVSAALAHAVAAAPIWQATPVDARADCLAR 703

Query: 721  AAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRPLGPV 780
            AA+L+EAQM +LMG++VREAGK+ +NA+AE+REA+DFLRYY+ Q+R+ FS+DTHRPLGPV
Sbjct: 704  AADLLEAQMHTLMGLVVREAGKSLANAVAEIREAIDFLRYYSTQIRDEFSNDTHRPLGPV 763

Query: 781  VCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLP 840
            VCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAVQLLP
Sbjct: 764  VCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAVQLLP 823

Query: 841  GRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIV 900
            G GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD  G+P+PLIAETGGQNAMIV
Sbjct: 824  GNGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPDGKPIPLIAETGGQNAMIV 883

Query: 901  DSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGNPDRL 960
            DSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM EL +GNPDRL
Sbjct: 884  DSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELAVGNPDRL 943

Query: 961  STDVGPVIDEEARGNIVRHIDAMRAKGRRVHQAD-PNGALSAACRNGTFVSPTLIELDSI 1019
            S DVGPVID +A+  I  H+  MR KGR+V Q   P+G     C  GTFV PTLIELDSI
Sbjct: 944  SIDVGPVIDLDAKRGIDAHVATMREKGRKVEQLPMPDG-----CAQGTFVPPTLIELDSI 998

Query: 1020 EELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNL 1079
            +EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++ RA VGN+
Sbjct: 999  DELKREVFGPVLHVVRYRRSQLDKLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHVGNI 1058

Query: 1080 YVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDTVGGAD 1139
            YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P      + +A   V  A 
Sbjct: 1059 YVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLAQA--LVADAP 1116

Query: 1140 ETGPVRRTLTETLATLKEWAQRESAALPGLVAACERFAAASAAGLSVTLPGPTGERNTYT 1199
                     +  L   ++W   E    P L A C+ + +   AG +  L GPTGERNTYT
Sbjct: 1117 NAAENSDNPSAALTAYRDWLIAEQQ--PVLAARCDGYLSHMPAGATAVLSGPTGERNTYT 1174

Query: 1200 LLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRVRLVADW 1259
            L PR  VLC+A   +   VQ AA LA G++A++ E      L A+LP +++SR  +    
Sbjct: 1175 LGPRGTVLCIASTASGARVQFAAALATGNRALF-EGAAGEQLVAQLPASLKSRASVK--- 1230

Query: 1260 SAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-----HGEPNIAIERLLIER 1314
             + D  FDAVL  GDSD+L A+ +++A RPGPI+SVQG+A      G+ + A+ERLL ER
Sbjct: 1231 KSADATFDAVLFEGDSDELLALVKEVAKRPGPIVSVQGVAARALESGDEDYALERLLTER 1290

Query: 1315 SLSVNTAAAGGNASLMTIG 1333
            S+SVNTAAAGGNA+LMTIG
Sbjct: 1291 SVSVNTAAAGGNANLMTIG 1309


Lambda     K      H
   0.318    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3982
Number of extensions: 147
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1333
Length of database: 1309
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1260
Effective search space:  1617840
Effective search space used:  1617840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate BPHYT_RS19355 BPHYT_RS19355 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.27297.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   6.5e-243  792.6   0.6   6.5e-243  792.6   0.6    1.8  2  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  BPHYT_RS19355 bifunctional proli


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS19355  BPHYT_RS19355 bifunctional proline dehydrogenase/pyrroline-5-carboxylate deh
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.6   0.6  6.5e-243  6.5e-243       1     499 [.     600    1099 ..     600    1100 .. 0.99
   2 ?   -1.2   0.1     0.028     0.028     179     217 ..    1193    1231 ..    1170    1246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 792.6 bits;  conditional E-value: 6.5e-243
                                TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqv 68  
                                               +lyg  r ns+G+dl+ne++l+sl++ ll++a++ ++aap+++++  a+g a+ v+npad++d+vG+v
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  600 NLYGAERLNSMGLDLSNEHRLASLSSALLASAHHPWRAAPMLEDNEIAVGVARDVRNPADHRDLVGTV 667 
                                               59****************************************************************** PP

                                TIGR01238   69 seadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevr 136 
                                                ea  ++v++a+  avaa+++w+at+ + ra +l r+adlle +m +l++l+vreaGk+l na+ae+r
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  668 VEATPEHVSAALAHAVAAAPIWQATPVDARADCLARAADLLEAQMHTLMGLVVREAGKSLANAVAEIR 735 
                                               ******************************************************************** PP

                                TIGR01238  137 eavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaa 204 
                                               ea+dflryy+ q++d+++++++++lG+vvcispwnfplaif+Gq+aaalaaGntv+akpaeqt+liaa
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  736 EAIDFLRYYSTQIRDEFSNDTHRPLGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAA 803 
                                               ******************************************************************** PP

                                TIGR01238  205 ravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpl 269 
                                               +av +l+eaGvpag++qllpG+Ge+vGaal +d+r + v+ftGstevarlink+l+ r d++   +pl
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  804 QAVRILREAGVPAGAVQLLPGNGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPDgkpIPL 871 
                                               ************************************************************87777*** PP

                                TIGR01238  270 iaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgk 337 
                                               iaetGGqnamivds+alaeqvvadvl+s+fdsaGqrcsalrvlc+q+dvadr+l+++ Gam el vg+
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  872 IAETGGQNAMIVDSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELAVGN 939 
                                               ******************************************************************** PP

                                TIGR01238  338 pirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkev 405 
                                               p rl  dvGpvid +ak+ + ah+  m++k++kv q+ + d   + +gtfv+ptl+eld++delk+ev
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355  940 PDRLSIDVGPVIDLDAKRGIDAHVATMREKGRKVEQLPMPD--GCAQGTFVPPTLIELDSIDELKREV 1005
                                               ****************************************9..9************************ PP

                                TIGR01238  406 fGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqp 473 
                                               fGpvlhvvry++++ldk++++i ++GygltlG+h+ri+et++++ +ra+vGn+yvnrn++GavvGvqp
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355 1006 FGPVLHVVRYRRSQLDKLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHVGNIYVNRNVIGAVVGVQP 1073
                                               ******************************************************************** PP

                                TIGR01238  474 fGGeGlsGtGpkaGGplylyrltrvr 499 
                                               fGGeGlsGtGpkaGG+lyl+rl+ +r
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355 1074 FGGEGLSGTGPKAGGALYLQRLLATR 1099
                                               **********************9765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.028
                                TIGR01238  179 GqiaaalaaGntviakpaeqtsliaaravellqeaGvpa 217 
                                                q aaala+Gn  +   a    l+a+   +l   a v  
  lcl|FitnessBrowser__BFirm:BPHYT_RS19355 1193 VQFAAALATGNRALFEGAAGEQLVAQLPASLKSRASVKK 1231
                                               4889**************9999**999988888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1309 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 24.61
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources