Alignments for a candidate for put1 in Desulfovibrio bastinii DSM 16055

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Desulfovibrio bastinii DSM 16055

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_027179221.1 G496_RS0110290 L-glutamate gamma-semialdehyde dehydrogenase

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_000429985.1:WP_027179221.1
          Length = 1012

 Score =  411 bits (1057), Expect = e-118
 Identities = 296/910 (32%), Positives = 468/910 (51%), Gaps = 62/910 (6%)

Query: 178  VIRQAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFN 237
            V+ + + + ++ M +QF++G+   EA+K     RK G+    D+LGEA ++ ++A  Y +
Sbjct: 107  VLNKTIRSNIEGMARQFIIGQKASEAVKGIRKLRKDGFAFVLDLLGEATVSAEEASAYRD 166

Query: 238  DYANAITELGAQ-----------SYNENESPRPTISIKLSALHPRYE-VANEDRVLTELY 285
             Y   +  +  +             +   +P+  +++K SA + + + VA ED V   + 
Sbjct: 167  GYMEVLEAIHKECDKWSALDASGDLDWGNAPKVNVAVKPSAFYSQAKPVAFEDTV-QGMV 225

Query: 286  DTVIRLIKLARGLNIGISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRA 345
            D++  + K    +N  + ID E ++  E +++L+++L        +  +GIV QAY K  
Sbjct: 226  DSIEPVYKKIMDMNGFMCIDMEALEYKEATIELYKRL--RKKYPEYEYIGIVFQAYLKST 283

Query: 346  LPVLVWLTRLAKEQGDEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACA 405
               +  +   A+E    I +RLVKGAYWDSE   A+Q  +   P++TRK  +D++Y   A
Sbjct: 284  ADDVAGMIEWAREVNLPISIRLVKGAYWDSETVIAKQ-NDWPVPVHTRKPESDLAYEQIA 342

Query: 406  RYLLSDATRGAIYPQFASHNAQTVAAISDMA-----GDRNHEFQRLHGMGQELYDTILSE 460
            + +L +      +   ASHN +T++AI +MA      +  +EFQ L+GM + +   +L  
Sbjct: 343  KMILEN--HDICHYACASHNIRTISAIMEMAIEMGVPEDRYEFQVLYGMAEPVRKGLLKV 400

Query: 461  AGAKAVRIYAPIGAHKDLLP---YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTL 517
            A  K VR+Y P G   DL+P   YLVRRLLEN AN SF+ +    +  IE L+ +P KTL
Sbjct: 401  A--KRVRLYCPYG---DLIPGMAYLVRRLLENTANESFLKQTFADEADIEILLENPAKTL 455

Query: 518  TGYKTLANNKIVLPTDIFGSDRKNSKGLN-------------MNIISEAEPFFAALDKFK 564
               + ++ +    P       R   +G+N               I SE + F  A++  +
Sbjct: 456  E--REISESPEPKP-----DTRPRYRGINGELEPFNNFPPVDFTIKSERDAFVEAIESVR 508

Query: 565  STQWQAGPL-VNGQTLTGEHKT-VVSPFDTTQTVGQVAFADKAAIEQAVASADAAFATWT 622
                +  PL +NG+ +T E      +P DT + +G V  A    ++QA+A A  A+  W 
Sbjct: 509  GNIGKKYPLYINGKEVTTEDTIDSYNPADTAEIIGTVCQAGIPEVDQAIAGAKDAYLKWR 568

Query: 623  RTPVEVRASALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKK 682
                  RA  L   A   +EN  EL AL   E GK       +V EA+DF  YYA +  +
Sbjct: 569  DVSPRERAQVLLDAARYCKENIYELSALQVVEVGKQWSQAHGDVAEAIDFMEYYAREMIR 628

Query: 683  LMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVSAALAAGNTVVAKPAEQ 742
            L   P  +    GEL++ F QG+GV   I+PWNFP AI +G VSAA+  G  VV KP+  
Sbjct: 629  L-GDPRRMGNAPGELSQYFYQGKGVAAVIAPWNFPFAISVGMVSAAIVCGCPVVYKPSGL 687

Query: 743  TSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTADERIGGVCFTGSTGTAKLINRT 802
            +S IGY  V++   AGIP  V  Y+PG G+ +G+ L     I  + FTGS      I   
Sbjct: 688  SSCIGYGLVEMFKAAGIPDGVFNYIPGRGSVMGDHLVDSPDISVIAFTGSMEVGLRIQER 747

Query: 803  LAN---REGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSSFTSAGQRCSALRVLFLQ 859
             A     +     +IAE GG+NA+++D  +  ++ V  V+ S+F   GQ+CSA   + + 
Sbjct: 748  AAKVHPGQEQCKKVIAEMGGKNAIIIDDDADLDEAVLGVLYSAFGYQGQKCSACSRVIVL 807

Query: 860  EDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKANLDAHIDHIKQVGK-LIKQM 918
            + I DR +  L  A   + +G   +    +GPV+D  A+ N+ ++ID  +Q G+ L+K+ 
Sbjct: 808  DSIYDRFVHRLTEAAKSVKLGPADNPDNYMGPVVDKAAQKNVLSYIDIAEQEGRILVKRE 867

Query: 919  SLPAGTENGHFVSPTAVE--IDSIKVLEKEHFGPILHVIRYKASELAHVIDEINSTGFGL 976
                    G +V  T VE      ++ ++E FGP+L V+R  A +    +D  NST FGL
Sbjct: 868  VSDELKAKGCYVPMTIVENITKEQRIAQEEIFGPVLAVMR--AKDFDEALDIANSTKFGL 925

Query: 977  TLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTR 1036
            T  I+SR+  H  + A +  VGN+Y+N+  +GA+V    FGG  +SG G K+GGP YL +
Sbjct: 926  TGSIYSRSPKHLEKGAREFRVGNLYLNKVSVGALVERHSFGGFKMSGVGSKSGGPDYLLQ 985

Query: 1037 FVTEKTRTNN 1046
            F+  +    N
Sbjct: 986  FMDPRIVCEN 995


Lambda     K      H
   0.317    0.133    0.377 

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: 2087
Number of extensions: 93
Number of successful extensions: 8
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: 1064
Length of database: 1012
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 967
Effective search space:   985373
Effective search space used:   985373
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 (21.6 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. 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 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