GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Shewanella amazonensis SB2B

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>lcl|FitnessBrowser__SB2B:6938545 Sama_2648 aldehyde dehydrogenase
           (RefSeq)
          Length = 498

 Score =  579 bits (1492), Expect = e-170
 Identities = 283/489 (57%), Positives = 357/489 (73%), Gaps = 4/489 (0%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           W+  A  L I  R FING Y  A   ETF+ + PV    L ++A  +  D D A++ AR 
Sbjct: 10  WEAMAQRLEINGRAFINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARA 69

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
           VFE G WSL SP KRK V+ + A+L+EAHA+ELALLETLD GKPI HS   D+ GAARAI
Sbjct: 70  VFESGVWSLQSPVKRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAI 129

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW  EAIDK+Y E+A T  +E+ MI REPVGV+AAIVPWNFP+L+ CWKLGPALA GNSV
Sbjct: 130 RWSGEAIDKIYDELAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSV 189

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           +LKPSEKSPL+AIR+A LAKEAGLPDGVLNV+ GFGH  GQAL+ H D+D + FTGST+ 
Sbjct: 190 VLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKI 249

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
            KQL+  AG SNMKRVWLEAGGKS NIVF D PDL+ AA A A+ I +NQG+VC AG+RL
Sbjct: 250 AKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRL 309

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+E  + DE + L+ ++ + WQPGHPLDPATT G ++D    D+V  +I+ G  +G  L+
Sbjct: 310 LVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLM 369

Query: 369 DGRNAGLAAA----IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G +  LA      + PT+F  V     ++REEIFGPV+ V  F   ++A+ +AND+ YG
Sbjct: 370 CGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYG 429

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484
           L A VWT D+S+AH+ ++ L++G V++N+Y+ GDMT PFGGYKQSGNGRDKSLHA EK+T
Sbjct: 430 LAAGVWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYT 489

Query: 485 ELKTIWISL 493
           E+K  WI+L
Sbjct: 490 EVKATWIAL 498


Lambda     K      H
   0.317    0.133    0.389 

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: 665
Number of extensions: 18
Number of successful extensions: 2
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: 495
Length of database: 498
Length adjustment: 34
Effective length of query: 461
Effective length of database: 464
Effective search space:   213904
Effective search space used:   213904
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: 52 (24.6 bits)

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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