GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella amazonensis SB2B

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 6938906 Sama_3009 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P76217
         (492 letters)



>FitnessBrowser__SB2B:6938906
          Length = 486

 Score =  589 bits (1518), Expect = e-173
 Identities = 285/484 (58%), Positives = 369/484 (76%)

Query: 1   MTLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAE 60
           MT +ING W+ G+G     +NP +GEV+WQG  A  AQV+ A  AAR A   W  L F  
Sbjct: 1   MTQFINGQWLAGEGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEG 60

Query: 61  RHAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQR 120
           R A+VE +   LE+NKAEL  +IA+ETGKPRWE ATE  AMI KI +S+ AYH RTG + 
Sbjct: 61  RQAIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEV 120

Query: 121 SEMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAV 180
           +E   G A LRH+PHGV+AVFGPYNFPGHLPNGHIVPALLAGNT++FKPSELTP   E +
Sbjct: 121 NEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180

Query: 181 MRLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKIL 240
           ++LW++AGLP GV+NLVQG  ETG+AL++   LDGL FTGS+ TG+ LH+Q +G P KIL
Sbjct: 181 LKLWEKAGLPAGVINLVQGEVETGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVA 300
           ALEMGGNNPLI+  V+D  AA+H  IQSAF+++GQRCTCARRL ++ GA+GD  LA LV 
Sbjct: 241 ALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAGLVE 300

Query: 301 VSQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
             + +  G W+ +PQPF+G +ISE AA+ ++ A + L  +G + L+    LQAGT L++P
Sbjct: 301 AVKAIKVGPWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMTHLQAGTGLVSP 360

Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420
           G+I++T V  +PDEE FGPLL+V RY +FDEAIR+AN+TR+GLS G+++ ++  ++  L 
Sbjct: 361 GLIDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILADDKADYEYFLA 420

Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480
             RAGIVNWNK +TGA+  APFGG+GASGNHR SA+YAADYCA+P+AS+E+DS+TLPA+L
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASMEADSVTLPASL 480

Query: 481 NPGL 484
           +PGL
Sbjct: 481 SPGL 484


Lambda     K      H
   0.318    0.134    0.412 

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: 776
Number of extensions: 28
Number of successful extensions: 1
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: 492
Length of database: 486
Length adjustment: 34
Effective length of query: 458
Effective length of database: 452
Effective search space:   207016
Effective search space used:   207016
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 (21.7 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