GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH 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)



>FitnessBrowser__ANA3:7023012
          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:

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