GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6938545
          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:

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