GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Acidithiobacillus ferrooxidans ATCC 23270

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_000021485.1:WP_012607209.1
          Length = 506

 Score =  285 bits (728), Expect = 3e-81
 Identities = 186/488 (38%), Positives = 256/488 (52%), Gaps = 15/488 (3%)

Query: 7   QNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRK 66
           ++ Y NFI G+WV    G    V  P +          STAED+E A+ AA+     W K
Sbjct: 16  KSKYDNFIGGKWVAPVKGQYFDVITPINGKSYT-QAARSTAEDIELALDAAHAIADKWGK 74

Query: 67  LTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEA-KGETARGIAILRYYAGEGMR 125
            + AER   L K AD +E  LE +A   T + GK + E    +    +   RY+AG    
Sbjct: 75  TSPAERANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRA 134

Query: 126 KTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATET 185
           + G  I   D++ + +    PLGVVG I PWNFP+ +  WK+APAL  GN VV+KPA  T
Sbjct: 135 QEGG-ISDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAEST 193

Query: 186 AVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAA 245
            ++   +     +  LP GV+N+V G G   G  LA    +  + FTGS   G++I QAA
Sbjct: 194 PISILILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAA 252

Query: 246 LARGAKYQLEMGGKNP------VIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQS 299
                   LE+GGK+P      V+  DD+ L+ A E ++  AF   G+ CT  SR ++Q 
Sbjct: 253 ANSLIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAFNQ-GEVCTCPSRALIQE 311

Query: 300 GIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGG- 358
            IY++F E+ L R K I  G+ L  +  +G  ASK QL   LSY++ GKQEGA +LIGG 
Sbjct: 312 SIYDKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGS 371

Query: 359 EKLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418
           + + +G    GYYVQP +F    ++M I QEEIFGPV+A+       EAL+IAND  +GL
Sbjct: 372 QAIVDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGL 430

Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478
            A +++ N          I AG V IN   A     A FGG K+S    RE  +   D +
Sbjct: 431 GAGVWSRNGNVAYRMGRAIKAGRVWINCYHA-YPAHAAFGGYKESGI-GRETHKVMLDHY 488

Query: 479 TAIKTVFV 486
              K + V
Sbjct: 489 QQTKNLLV 496


Lambda     K      H
   0.315    0.132    0.374 

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: 580
Number of extensions: 28
Number of successful extensions: 7
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: 488
Length of database: 506
Length adjustment: 34
Effective length of query: 454
Effective length of database: 472
Effective search space:   214288
Effective search space used:   214288
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 (21.5 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