GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Acidithiobacillus ferrooxidans ATCC 23270

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein

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



>NCBI__GCF_000021485.1:WP_012536996.1
          Length = 506

 Score =  283 bits (723), Expect = 1e-80
 Identities = 181/483 (37%), Positives = 254/483 (52%), Gaps = 19/483 (3%)

Query: 5   QRFDNYINGQWVAGA--DYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTS 62
           +R+DN+I G+WVA    +Y  N++P        +  ++    +  A+DAA AA  AW  +
Sbjct: 17  ERYDNFIGGRWVAPVRGEYFDNISPIN-GKPFCQIPRSSAEDIELALDAAHAAKDAWGRT 75

Query: 63  GIQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRL 121
            + AR + L K+   I A  E L      + GK + E +  +V  + + F++FAG CLR 
Sbjct: 76  SVTARSNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAG-CLRA 134

Query: 122 SGDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVP 181
               +  +          E LGVVG I PWNFP+ +  WK+APALA GNCVV+KPAE  P
Sbjct: 135 QEGTIGEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTP 194

Query: 182 GCAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCV 241
                + E+I+    PAGV N+V G G   G  L  S ++  I+FTGS  VG  I     
Sbjct: 195 ASILVMMELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAA 253

Query: 242 SRQAKVQLEMGGKNPQIIL------DDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAG 295
                  +E+GGK+P I        +DA + +AVE +V  AF++ G+ CT  SRL++   
Sbjct: 254 ENIIPSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAV-LAFFNQGEVCTCPSRLLIQES 312

Query: 296 IHDQFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGL 355
           I+++F+  + ER   IK G+ L +   +G   SQ Q D+ L YI IG+ EGA +++GG +
Sbjct: 313 IYEKFIGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGAV 372

Query: 356 VTCDT---EGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLS 412
            T      EGYY+ PTL   +   MR+ +EEIFGPV +V    D   ALA+AND EFGL 
Sbjct: 373 ETMSADYCEGYYIQPTLLKGTN-NMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLG 431

Query: 413 AGIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYT 472
           AG+ T  +  A    R  QAG V  N        H  FGG K S  G RE  +   + Y 
Sbjct: 432 AGVWTRDMNRAYRMGRGIQAGRVWTNCYHM-YPAHAAFGGYKKSGVG-RETHKMMLDHYQ 489

Query: 473 VVK 475
             K
Sbjct: 490 QTK 492


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: 516
Number of extensions: 32
Number of successful extensions: 6
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 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