GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Acidithiobacillus ferrooxidans ATCC 23270

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein

Query= BRENDA::P23883
         (495 letters)



>NCBI__GCF_000021485.1:WP_012536996.1
          Length = 506

 Score =  331 bits (849), Expect = 3e-95
 Identities = 187/483 (38%), Positives = 282/483 (58%), Gaps = 16/483 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI G + A    E F+ + P+   P  +I R  + DI+ A+ AA     +  W  +S   
Sbjct: 22  FIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIELALDAAHAA--KDAWGRTSVTA 79

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L K+AD ++A+ E LA+ ET D GK +R +L  D+P ++   R++A  +    G +
Sbjct: 80  RSNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPLSSDHFRYFAGCLRAQEGTI 139

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
                + +A    EP+GV+  I+PWNFPLL+ CWKL PALAAGN V+LKP+E++P S + 
Sbjct: 140 GEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASILV 199

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           +  L  +  LP GVLNVV G+G EAG+AL+    I  IAFTGST  G  ++K A + N+ 
Sbjct: 200 MMELIADL-LPAGVLNVVNGYGVEAGKALATSKRIAKIAFTGSTPVGSLIMKYAAE-NII 257

Query: 263 RVWLEAGGKSANIVFADCPDLQQA----ASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
              +E GGKS NI FAD  D + A    A   A   F+NQG+VC   +RLL++ESI ++F
Sbjct: 258 PSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLAFFNQGEVCTCPSRLLIQESIYEKF 317

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA 378
           + ++ +++   + G+PLD    +G        D + S+I+ G+ +G  ++ G      +A
Sbjct: 318 IGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGKDEGAEVITGGAVETMSA 377

Query: 379 -------IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
                  I PT+    + N  + +EEIFGPV+ VT F  E +AL +AND ++GLGA VWT
Sbjct: 378 DYCEGYYIQPTLLKGTN-NMRVFQEEIFGPVVSVTTFKDEAEALAIANDIEFGLGAGVWT 436

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           RD++RA+RM R ++AG V+ N Y+       FGGYK+SG GR+     L+ + + K + +
Sbjct: 437 RDMNRAYRMGRGIQAGRVWTNCYHMYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLV 496

Query: 492 SLE 494
           S +
Sbjct: 497 SYD 499


Lambda     K      H
   0.317    0.133    0.389 

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: 521
Number of extensions: 18
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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