Alignments for a candidate for putA in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Paraburkholderia phymatum STM815

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_012402366.1 BPHY_RS15380 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase

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



>NCBI__GCF_000020045.1:WP_012402366.1
          Length = 1320

 Score = 1744 bits (4516), Expect = 0.0
 Identities = 923/1357 (68%), Positives = 1064/1357 (78%), Gaps = 61/1357 (4%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RLK  A  ++RTPHWLIKQAIF YLE++E G +P E S    G 
Sbjct: 1    MASTTLGVKVDDLLRTRLKDAATRLERTPHWLIKQAIFAYLEKIEHGQLPAELS----GH 56

Query: 61   EGAADGAD-AFDGAASDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLEQAR 119
             GA + AD A D   SDG + PFLEFAQSVQPQSVLRAAITAAYRRPE ECVP L+ QAR
Sbjct: 57   HGATELADGAADPDESDG-LHPFLEFAQSVQPQSVLRAAITAAYRRPEPECVPFLIGQAR 115

Query: 120  LPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEALLRI 179
            LP   A    AMA  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEALLRI
Sbjct: 116  LPANIANDVQAMASKLVEALRSKSTGGG----VEGLIHEFSLSSQEGVALMCLAEALLRI 171

Query: 180  PDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKALTRI 239
            PD+ATRDALIRDKIS  +W+SH+G +PS+FVNAATWGL+ TGKLV T++E GLS ALTR+
Sbjct: 172  PDRATRDALIRDKISKGDWRSHVGHAPSLFVNAATWGLMITGKLVTTNSETGLSSALTRM 231

Query: 240  IGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAMTEA 299
            IGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALAN+RK+EA GFRYSYDMLGEAA TEA
Sbjct: 232  IGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANSRKFEARGFRYSYDMLGEAATTEA 291

Query: 300  DAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGRLKS 359
            DAQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALHPRYSR+Q ER + EL  R+++
Sbjct: 292  DAQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHPRYSRSQQERTMSELLPRVRA 351

Query: 360  LTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVID 419
            L +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PEL GWNGIGFVVQ YQKRCPFVID
Sbjct: 352  LAILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELQGWNGIGFVVQAYQKRCPFVID 411

Query: 420  YLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLS 479
            Y++DLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+KLL 
Sbjct: 412  YIVDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKKLLG 471

Query: 480  VPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNR 539
             PD +YPQFATHNAHTL+AIY +AG NYYPGQYEFQCLHGMGEPLY++V G     K NR
Sbjct: 472  APDAVYPQFATHNAHTLSAIYHLAGQNYYPGQYEFQCLHGMGEPLYEEVTG---RDKLNR 528

Query: 540  PCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADE 599
            PCR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+T+ + +LVADPV        DE
Sbjct: 529  PCRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETVPVQDLVADPV--------DE 580

Query: 600  GA----LGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLL 655
             A    LG PH +I  PR LYG  R NS G+DLSNEHRLASLSSALLA  +    A P+L
Sbjct: 581  AAKIVPLGAPHAKIPLPRNLYGAERTNSMGLDLSNEHRLASLSSALLASANHPWRAAPML 640

Query: 656  -GTEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVR 714
             G E A G    +   VRNPSD RD+VG V EA+   V AAL  AV AAPIWQATP + R
Sbjct: 641  EGNEIAVG----RARDVRNPSDHRDLVGTVVEATPEHVSAALAHAVAAAPIWQATPVEAR 696

Query: 715  AAALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTH 774
            A  L RAA+L+EAQM +LMG++VREAGK+  NA+AE+REA+DFLRYY++Q+R+ FS+DTH
Sbjct: 697  ADCLARAADLLEAQMHTLMGLVVREAGKSLPNAVAEIREAIDFLRYYSSQIRDEFSNDTH 756

Query: 775  RPLGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAG 834
            RPLGPVVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAG
Sbjct: 757  RPLGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAG 816

Query: 835  AVQLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGG 894
            AVQLLPG GETVGAALV DAR + VMFTGSTEVARL+ ++++ RLD  G+P+PLIAETGG
Sbjct: 817  AVQLLPGDGETVGAALVADARTRAVMFTGSTEVARLINKTLSNRLDPDGKPIPLIAETGG 876

Query: 895  QNAMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTM 954
            QNAMIVDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM EL +
Sbjct: 877  QNAMIVDSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMKELAV 936

Query: 955  GNPDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQAD-PNGALSAACRNGTFVSPTL 1013
            GNPDRLS DVGPVID EA+  I  HI +MR KGR+V Q   P+G     C  GTFV PTL
Sbjct: 937  GNPDRLSIDVGPVIDAEAKRGIDAHIASMREKGRKVTQMPMPDG-----CAAGTFVPPTL 991

Query: 1014 IELDSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVER 1073
            IELD+I+EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++ R
Sbjct: 992  IELDNIDELKREVFGPVLHVVRYRRSALDKLLEQIRATGYGLTLGIHTRIDETIAHVIGR 1051

Query: 1074 AEVGNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPL---DAVARVVR 1130
            A VGN+YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P     ++AR + 
Sbjct: 1052 AHVGNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLARTLM 1111

Query: 1131 ASDTVGGAD-------ETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASA 1181
               + G A+                   L TL++W  A+RE    P L A C+ + +   
Sbjct: 1112 VDASQGAANGGQSAAQNGNAASDNPAAALTTLRDWLIAERE----PVLAARCDGYLSHIP 1167

Query: 1182 AGLSVTLPGPTGERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARAL 1241
            AG +  L GPTGERNTYTL  R  VLC+A   +   VQ AA LA G++A++ E      L
Sbjct: 1168 AGATAVLAGPTGERNTYTLGARGTVLCVASTASGARVQFAAALATGNKALF-EGAAGEQL 1226

Query: 1242 FARLPKAVQSRVRLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-- 1299
            +A LP +++    +  +    +  FDA L  GDSD+L A+ + +A R GPI+SVQG+A  
Sbjct: 1227 YAALPPSLKQYASVKKN---AEASFDAALFEGDSDELLALVKDIAKRAGPIVSVQGVAAR 1283

Query: 1300 ---HGEPNIAIERLLIERSLSVNTAAAGGNASLMTIG 1333
                G+ + A+ERLL ERS+SVNTAAAGGNA+LMTIG
Sbjct: 1284 ALESGDEDYALERLLTERSVSVNTAAAGGNANLMTIG 1320


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: 4023
Number of extensions: 157
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: 1320
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1271
Effective search space:  1631964
Effective search space used:  1631964
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 WP_012402366.1 BPHY_RS15380 (trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde 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.32171.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-244  797.0   0.8   5.2e-244  796.2   0.8    1.3  1  lcl|NCBI__GCF_000020045.1:WP_012402366.1  BPHY_RS15380 trifunctional trans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012402366.1  BPHY_RS15380 trifunctional transcriptional regulator/proline dehydrogenase/
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  796.2   0.8  5.2e-244  5.2e-244       1     499 [.     599    1098 ..     599    1099 .. 0.99

  Alignments for each domain:
  == domain 1  score: 796.2 bits;  conditional E-value: 5.2e-244
                                 TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67  
                                                +lyg  r+ns+G+dl+ne++l+sl++ ll++a++ ++aap+++++  a+g a+ v+np d++d+vG+
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  599 NLYGAERTNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLEGNEIAVGRARDVRNPSDHRDLVGT 665 
                                                59***************************************************************** PP

                                 TIGR01238   68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134 
                                                v ea  ++v++a+  avaa+++w+at+ + ra +l r+adlle +m +l++l+vreaGk+l na+ae
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  666 VVEATPEHVSAALAHAVAAAPIWQATPVEARADCLARAADLLEAQMHTLMGLVVREAGKSLPNAVAE 732 
                                                ******************************************************************* PP

                                 TIGR01238  135 vreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsl 201 
                                                +rea+dflryy+ q++d+++++++++lG+vvcispwnfplaif+Gq+aaalaaGntv+akpaeqt+l
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  733 IREAIDFLRYYSSQIRDEFSNDTHRPLGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPL 799 
                                                ******************************************************************* PP

                                 TIGR01238  202 iaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.. 266 
                                                iaa+av +l+eaGvpag++qllpG Ge+vGaal +d+r + v+ftGstevarlink+l++r d++  
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  800 IAAQAVRILREAGVPAGAVQLLPGDGETVGAALVADARTRAVMFTGSTEVARLINKTLSNRLDPDgk 866 
                                                ***************************************************************8777 PP

                                 TIGR01238  267 .vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamde 332 
                                                 +pliaetGGqnamivds+alaeqvvadvl+s+fdsaGqrcsalrvlc+q+dvadr+l+++ Gam+e
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  867 pIPLIAETGGQNAMIVDSSALAEQVVADVLQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMKE 933 
                                                7****************************************************************** PP

                                 TIGR01238  333 lkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddld 399 
                                                l vg+p rl  dvGpvidaeak+ + ahi  m++k++kv+q+ + d   +  gtfv+ptl+eld++d
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  934 LAVGNPDRLSIDVGPVIDAEAKRGIDAHIASMREKGRKVTQMPMPD--GCAAGTFVPPTLIELDNID 998 
                                                ********************************************99..9****************** PP

                                 TIGR01238  400 elkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvG 466 
                                                elk+evfGpvlhvvry+++ ldk++++i a+GygltlG+h+ri+et++++ +ra+vGn+yvnrn++G
  lcl|NCBI__GCF_000020045.1:WP_012402366.1  999 ELKREVFGPVLHVVRYRRSALDKLLEQIRATGYGLTLGIHTRIDETIAHVIGRAHVGNIYVNRNVIG 1065
                                                ******************************************************************* PP

                                 TIGR01238  467 avvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 
                                                avvGvqpfGGeGlsGtGpkaGG+lyl+rl+ +r
  lcl|NCBI__GCF_000020045.1:WP_012402366.1 1066 AVVGVQPFGGEGLSGTGPKAGGALYLQRLLATR 1098
                                                *****************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1320 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 15.57
//
[ok]

This GapMind analysis is from Sep 24 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:

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