Alignments for a candidate for gadh1 in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for gadh1 in Jannaschia aquimarina GSW-M26

Align Gluconate 2-dehydrogenase flavoprotein; GA 2-DH dehydrogenase subunit; GADH dehydrogenase subunit; EC 1.1.99.3 (characterized)
to candidate WP_043918080.1 jaqu_RS06245 GMC family oxidoreductase

Query= SwissProt::O34214
         (615 letters)



>NCBI__GCF_000877395.1:WP_043918080.1
          Length = 589

 Score =  535 bits (1379), Expect = e-156
 Identities = 277/596 (46%), Positives = 373/596 (62%), Gaps = 14/596 (2%)

Query: 22  VANELKKVDAVVVGFGWAGAIMAKELTEAGLNVVALERGPHRDTYPDGAYPQSIDELTYN 81
           +A  L + DAV+VGFGW GAI AKELT+AGL+VVALERGP      D A  +  D LTY+
Sbjct: 1   MARTLPRTDAVIVGFGWTGAIAAKELTDAGLSVVALERGPAYGQ-DDFATRRMHDGLTYS 59

Query: 82  IRKKLFQDLSKSTVTIRHDASQTAVPYRQLAAFLPGTGTGGAGLHWSGVHFRVDPVELNL 141
           +R  L   L + T+T R++  QTA+P R++ +F P  G GG+G  WSG   R  P +  L
Sbjct: 60  VRGGLATPLDRVTLTFRNNGDQTALPMRRIGSFNPSQGFGGSGNTWSGHSPRAYPSDFVL 119

Query: 142 RSHYEARYGKNFIPEGMTIQDFGVSYNELEPFFDQAEKVFGTSGSAWTIKGKMIGKEKGG 201
           RSHY  RYG +  PE MT QD+GV+++E+EP +D+ EKV   SG+A  ++G+   + +GG
Sbjct: 120 RSHYTERYGADIFPEHMTSQDWGVTWDEVEPGYDRFEKVAAVSGTAGNVRGE---RREGG 176

Query: 202 NFYAPDRSSDFPLPAQKRTYSAQLFAQAAESVGYHPYDMPSANTSGPYTNTYGAQMGPCN 261
           N Y  +RS DFPLPA +R    +LF + A+S+G +P+ +P AN S  YTN YG +MG C 
Sbjct: 177 NPYEGERSDDFPLPAFERNRPGRLFIETAQSMGLNPFPVPVANASEAYTNAYGVEMGRCV 236

Query: 262 FCGYCSGYACYMYSKASPNVNILPALRQEPKFELRNNAYVLRVNLTGDKKRATGVTYLDG 321
            CG+C G+AC   +K SP  +++PA+  +  FE R+   VLR+    D +  TGVTYL  
Sbjct: 237 LCGHCPGFACAYQAKGSPVNSVIPAIGGD--FEARSECEVLRIERAEDGRTVTGVTYLSP 294

Query: 322 QGREVVQPADLVILSAFQFHNVHLMLLSGIGQPYNPITNEGVVGRNFAYQNISTLKALFD 381
            G E+ QPAD+VIL A+ F NV L+LLSGIG  Y+P T EGVVGRN++YQ ++ ++A F+
Sbjct: 295 AGEELFQPADIVILGAYAFENVRLLLLSGIGAAYDPATGEGVVGRNYSYQTLANVEAFFE 354

Query: 382 KNTTTNPFIGAGGAGVAVDDFNADNFDHGP-----YGFVGGSPFWVNQAGTKPVSGLPTP 436
                NP I  G  G  +DD+ +DNFDH         F+GG        G  P++  PT 
Sbjct: 355 -GEAMNPQIAGGSQGTILDDYQSDNFDHAQALVDGRPFIGGGFIGPFNLGADPITYHPTA 413

Query: 437 KGTPNWGSQWKAAVADTYNHHISMDAHGAHQSYRANYLDLDPNYKNVYGQPLLRMTFDWQ 496
            G+P WG+ WK AV   Y + + ++ H + QSYR NYLDLDP Y++ YG+PLLRMTFD+ 
Sbjct: 414 PGSPPWGAGWKEAVVAGYQNRVGINVHASVQSYRGNYLDLDPTYRDAYGRPLLRMTFDFP 473

Query: 497 DNDIRMAQFMVGKMRKITEAMNPKMIIGGAKGPGTHFDTTVYQTTHMSGGAIMGEDPKTS 556
           DN+ RM +F++ +  +I   M    +   A G    +D TVYQTTH  GG  MG DP TS
Sbjct: 474 DNEQRMMRFLMDRAEEIAREMGASQV--RANGLKVPYDITVYQTTHNVGGTAMGADPGTS 531

Query: 557 AVNRYLQSWDVPNVFVPGASAFPQGLGYNPTGMVAALTYWSAKAIREQYLKNPGPL 612
            VN  LQ WD  N+FV G S FPQ +G NPT  +AAL Y S   +  +YL +P PL
Sbjct: 532 VVNTALQHWDAHNLFVLGGSVFPQNVGVNPTPTIAALAYHSLGRLTGEYLSDPRPL 587


Lambda     K      H
   0.317    0.135    0.416 

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: 1129
Number of extensions: 59
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: 615
Length of database: 589
Length adjustment: 37
Effective length of query: 578
Effective length of database: 552
Effective search space:   319056
Effective search space used:   319056
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: 53 (25.0 bits)

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 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