GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Acidithiobacillus ferrooxidans ATCC 23270

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= reanno::SB2B:6938906
         (486 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  143 bits (360), Expect = 2e-38
 Identities = 148/478 (30%), Positives = 220/478 (46%), Gaps = 56/478 (11%)

Query: 4   FINGQWLAG-EGKEMQSKNPANGEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQ 62
           FI G+W+A  +G+      P NG+   Q   +    ++ A+ AA     +W       R 
Sbjct: 22  FIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSPAERA 81

Query: 63  AIVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTG----- 117
            I+    + +EAN   LA     + GKP  ET          I L+V  +    G     
Sbjct: 82  NILLKVADRIEANLELLAYAETVDNGKPIRETLN------ADIPLAVDHFRYFAGCVRAQ 135

Query: 118 ----TEVNEGAAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELT 173
               ++++E     A   H+P GVV    P+NFP  + +  + PAL AGN VV KP+E T
Sbjct: 136 EGGISDIDENTV--AYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAEST 193

Query: 174 P----KVAELMLKLWEKAGLPAGVINLVQG-EVETGKALASHPQLDGLFFTGSSRTGHLL 228
           P     +AEL+  L     LP GV+N+V G   E G  LA+  ++  + FTGS+ TG ++
Sbjct: 194 PISILILAELIADL-----LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVI 248

Query: 229 HQQYAGHPGKILALEMGGNNPLIV------KGVSDTRAAIHDIIQSAFISSGQRCTCARR 282
             Q A +      LE+GG +P I       K  S    AI  ++  AF + G+ CTC  R
Sbjct: 249 -AQAAANSLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSR 306

Query: 283 LYVEKGAEGDKLLAGLVEAVKAIKVG-PWNADPQPFMGSMISETAAKGMLDAQRNLLNLG 341
             +++    DK +   ++ +KAIK G P + +      +MI   A+K  L    + L+LG
Sbjct: 307 ALIQESIY-DKFMERCLDRIKAIKQGNPLDTN------TMIGAQASKEQLTKILSYLDLG 359

Query: 342 AK--SLVEMTHLQA-------GTGLVSPGLIDVTEVIELPDEEYFGPLLQVVRYTSFDEA 392
            +  + V +   QA       G   V P L      + +  EE FGP+L V  +    EA
Sbjct: 360 KQEGAQVLIGGSQAIVDGDLDGGYYVQPTLFKGHNKMRIFQEEIFGPVLAVTTFKDEAEA 419

Query: 393 IRLANDTRYGLSAGILADDKADYEYFLAR-IRAGIVNWNKQITGASGAAPFGGVGASG 449
           + +ANDT YGL AG+ + +  +  Y + R I+AG V W          A FGG   SG
Sbjct: 420 LSIANDTLYGLGAGVWSRN-GNVAYRMGRAIKAGRV-WINCYHAYPAHAAFGGYKESG 475


Lambda     K      H
   0.317    0.133    0.393 

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: 551
Number of extensions: 27
Number of successful extensions: 3
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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