Alignments for a candidate for putA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Stenotrophomonas chelatiphaga DSM 21508

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_057508189.1 ABB28_RS08325 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>NCBI__GCF_001431535.1:WP_057508189.1
          Length = 892

 Score =  831 bits (2147), Expect = 0.0
 Identities = 453/867 (52%), Positives = 582/867 (67%), Gaps = 31/867 (3%)

Query: 20  FFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSLIEAVRGRDNAVDTLDALLR 79
           F  AI+  +  DEA +++ELL  A       A ++  A  L+  VR R      ++A +R
Sbjct: 32  FRQAITDAWLKDEATHVSELLAQARLPADEQAQVQALAADLVARVRVRAKDQGAIEAFMR 91

Query: 80  QYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEWERHLGQSDNVLVNFAAWGL 139
           QY L ++EG++LMC+AEALLR+PD  TAD LIRDKL  A+W++H+G SD+VLVN + WGL
Sbjct: 92  QYDLGSEEGVLLMCVAEALLRIPDQDTADKLIRDKLADADWKKHMGGSDSVLVNASTWGL 151

Query: 140 VMTGKVV---DPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMKLMGKQFVLGRTISEAL 196
           ++TGK+V   D   AD        RL+ R GEPVIR A+ QAMK+MG QFV+GRTI EAL
Sbjct: 152 MLTGKLVQINDVTRAD--VPGAFKRLMGRVGEPVIRLAVRQAMKIMGHQFVMGRTIGEAL 209

Query: 197 KNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGAE-------PQVGKGPR 249
           +         Y YSFDMLGE ALT +DA +Y+ DYR+A+  +G +       P+      
Sbjct: 210 ERSHKGDNASYRYSFDMLGEGALTMKDALRYLEDYRRAIHAIGGDHKARGGRPEGDVNNA 269

Query: 250 PSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEADRLELSLEL 309
           P +SIKLSAL+PRYE A+R RVL +L   V ELA LA+   +G T+DAEEADRLELSL++
Sbjct: 270 PGISIKLSALYPRYEHAKRARVLQDLVPGVLELAQLAKSYGIGCTVDAEEADRLELSLDI 329

Query: 310 YEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVKGAYWDSEIK 369
            + +  D ++AGW  FG+V+QAY KR    + +L  + R  G R+ +RLVKGAYWD+EIK
Sbjct: 330 IDAVFSDASLAGWDGFGVVVQAYQKRTPYTIDFLADMARRNGRRLQVRLVKGAYWDAEIK 389

Query: 370 QCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTVSCILAMAEE 429
           + Q++G  GYPV+TRK+ TD SYLACA+ L        IYP FA+HNAHT++ I  +A+ 
Sbjct: 390 RAQIEGYPGYPVFTRKQNTDVSYLACAKRLFGHSD--AIYPMFATHNAHTIAAIRTIAKG 447

Query: 430 TAQPREFEFQRLHGMGDALYDTVI--EKYARNVRIYAPVGAHKDLLPYLVRRLLENGANS 487
                 +E Q+LHGMGD LY  V+  ++     R+YAPVG+H+DLLPYLVRRLLENGANS
Sbjct: 448 GV----YEHQKLHGMGDDLYAEVVPADRLGLPCRVYAPVGSHEDLLPYLVRRLLENGANS 503

Query: 488 SFVHQLVDPRVPVESLIDHPVTQLRRFAA--PGN---PRIPLPPALFGN----RKNSQGI 538
           SFV+++ D RV +  L+  PV  +  FAA  P N   P+IPLP  L  +    R NS GI
Sbjct: 504 SFVNRITDDRVAIAELVRDPVEMVSAFAAVSPSNIAHPKIPLPVNLLRSQNHDRNNSMGI 563

Query: 539 NMNIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASAD 598
           N+   N    LA      + + W AAP++ G T+ G    V  P +  +VVG  Q A A 
Sbjct: 564 NLANDNALRALAEQLNAAV-KPWTAAPLVPGATVTGASLPVTNPADTRQVVGHWQAADAA 622

Query: 599 QARQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDE 658
             ++A+    A  P WN TP  +RAA+LE   D LE   AE MALC  EAGKSL DG+ E
Sbjct: 623 TVQKALANAVAAQPAWNRTPATSRAAILEHAADQLEARIAEFMALCVKEAGKSLPDGVAE 682

Query: 659 VREAVDFCRYYAQQARLKLGR-EELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQI 717
           VREAVDF RYYA+QAR +    E+L  PTGE NEL   GRGVFVC+SPWNFPLAI+LGQ+
Sbjct: 683 VREAVDFLRYYAKQAREQFAHAEKLPSPTGESNELQLHGRGVFVCISPWNFPLAIFLGQV 742

Query: 718 TAALVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVV 777
            AAL AGN+V+AKPAEQT+LI   A++L+ +AG+P+  + FLPGDGAT+G     DPRV 
Sbjct: 743 AAALAAGNSVIAKPAEQTNLIGYYAVKLLLDAGVPEGVLQFLPGDGATVGAALTADPRVA 802

Query: 778 GVCFTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTS 837
           GV FTGSTDTAR INR +A ++  I  LIAETGGQNA I DS+ALPEQ++KDA+GSAFTS
Sbjct: 803 GVAFTGSTDTARAINRAMAARDAAIGVLIAETGGQNAFIADSSALPEQLVKDAIGSAFTS 862

Query: 838 AGQRCSALRVLYVQRDIADRVIDLLKG 864
           AGQRCSA RVL+VQ DIAD+V+ +L G
Sbjct: 863 AGQRCSAARVLFVQDDIADKVMTMLAG 889


Lambda     K      H
   0.319    0.136    0.396 

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: 2088
Number of extensions: 89
Number of successful extensions: 9
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: 1053
Length of database: 892
Length adjustment: 44
Effective length of query: 1009
Effective length of database: 848
Effective search space:   855632
Effective search space used:   855632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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