GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xacF in Shewanella sp. ANA-3

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)

Query= reanno::WCS417:GFF827
         (481 letters)



>lcl|FitnessBrowser__ANA3:7023012 Shewana3_0250 aldehyde
           dehydrogenase (RefSeq)
          Length = 506

 Score =  270 bits (691), Expect = 6e-77
 Identities = 170/467 (36%), Positives = 249/467 (53%), Gaps = 18/467 (3%)

Query: 5   QRFDNYINGQWVA--GADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTS 62
           +++ N+I G+WVA    DY  N +P    +   +  ++D   +  A+DAA AA  AW  +
Sbjct: 17  EKYANFIGGKWVAPVNGDYFENRSPVNGQNFC-KIPRSDYRDIELALDAAHAAKDAWGKT 75

Query: 63  GIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRL 121
            +  R + L ++   +    E L      E GK + E +  ++    + F++FAG C+R 
Sbjct: 76  SVTERANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAG-CIRA 134

Query: 122 SGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVP 181
                  +          E LGVVG I PWNFP+ + AWKIAPALA GNCVV+KPAE  P
Sbjct: 135 QEGSAADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTP 194

Query: 182 GCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCV 241
                L E+I     P G+ N+V G G   G  L  S ++  ++FTGS  VG  I     
Sbjct: 195 VSILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKCAA 253

Query: 242 SRQAKVQLEMGGKNPQI----ILDDAD--LKQAVELSVQSAFYSTGQRCTASSRLIVTAG 295
                  +E+GGK+P +    ++D  D  L +AVE  +  AF++ G+ CT  SR+++   
Sbjct: 254 ESLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVE-GMLLAFFNQGEVCTCPSRVLIQES 312

Query: 296 IHDQFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGL 355
           I+D+F+  +  R ++IK G+ L + T +G   SQ Q D+ L Y+ IG+ EGA+++ GG L
Sbjct: 313 IYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSL 372

Query: 356 VTCD---TEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLS 412
              +   ++GYY++PT+       MRI +EEIFGPV +V    D   ALA+ANDTE+GL 
Sbjct: 373 CQLEGDQSKGYYISPTIM-KGHNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLG 431

Query: 413 AGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG 459
           AG+ T  +  A    R  QAG V +N   A    H  FGG K S  G
Sbjct: 432 AGVWTRDMNRAQRLGRGIQAGRVWINCYHA-YPAHAAFGGYKKSGIG 477


Lambda     K      H
   0.318    0.134    0.390 

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: 535
Number of extensions: 31
Number of successful extensions: 5
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: 481
Length of database: 506
Length adjustment: 34
Effective length of query: 447
Effective length of database: 472
Effective search space:   210984
Effective search space used:   210984
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 preprint 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