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.5863.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: 00:00:00.03
# Mc/sec: 17.98
//
[ok]

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

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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:

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:

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:

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:

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