Alignments for a candidate for aldox-large in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Acidovorax sp. GW101-3H11

Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate Ac3H11_3591 Carbon-monoxide dehydrogenase form II, large subunit (EC 1.2.99.2)

Query= SwissProt::Q4J6M3
         (748 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3591
          Length = 795

 Score =  442 bits (1138), Expect = e-128
 Identities = 281/790 (35%), Positives = 423/790 (53%), Gaps = 46/790 (5%)

Query: 1   MTYTGKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNG 59
           + + G+S+KR  D +F+TG   Y DD+ + +  +A FVRSP+ HA I  I+ + A    G
Sbjct: 9   LPHIGESLKRKEDYRFLTGAGQYTDDVVLAAQCHAVFVRSPHAHAGINSINTSAAKAAPG 68

Query: 60  IVAVFSGKDINPMLKGGV--GVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQD 117
           ++ VF G D+      G+  G L    N    +        +  KV+YVG+ VA+V+ Q 
Sbjct: 69  VLGVFVGADVAADNINGLPCGWLITSTNGEPMKEPPHPILAQ-GKVRYVGDHVAMVVAQT 127

Query: 118 KYAVRDAIDRVNVEYEQLKPVIKMEDAEKDEVI---VHDELKTNVSYKIPF-KAGDIEKA 173
               RDA + V V+Y+ L  V+ + DA    V    +HD    N  +K      G ++ A
Sbjct: 128 LQQARDAAELVEVDYDVLPAVVNVADAAAGAVAGAALHDIAPDNHCFKWAIGDKGAVDAA 187

Query: 174 FSQADKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEF-ARIFG 230
           F+ A  V +++ IN RLIPN MEPR  +  Y    +  +++ S Q PH  R    A + G
Sbjct: 188 FAGAAHVTQLDLINNRLIPNAMEPRAAIGSYSRANDEYTLYVSNQNPHVERLLMTAFVMG 247

Query: 231 IPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARSN 289
           +PE K+RV  PDVGG FGSK+++ AE++ +  ++  L R ++W A RSE  L+ +  R +
Sbjct: 248 LPEHKVRVIAPDVGGGFGSKIYLYAEDVCLTWAAKKLNRNIKWVADRSESFLSDAHGRDH 307

Query: 290 VFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIESTA 348
           +   E+A+ KDG  L ++     +LGAYL+  A   PTI+   ++ G Y    + +E  +
Sbjct: 308 ISHAEMAMDKDGKFLAMRVHTHANLGAYLSTFASAVPTILYATLLAGQYTTPQVYVEVDS 367

Query: 349 VYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLRY 408
            +T T P+  YRGA RPEATY++ER+++  A ELGL    IR+RN I   PY  P  L+Y
Sbjct: 368 WFTNTAPVDAYRGAGRPEATYLLERLVTRCAWELGLSQDEIRKRNFITSFPYQTPVALQY 427

Query: 409 DTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP---------- 458
           D GDY           +            +KG + G+G + Y+E C   P          
Sbjct: 428 DIGDYHACMTQAQQLADVAGFAARKAASEAKGFKRGIGYSSYIEACGIAPSNIAGALGAR 487

Query: 459 ---WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVE 515
              +E GE++V   G+V V TG+  HGQG ET  AQ+VA  L IP+E + +V GDT  V 
Sbjct: 488 AGLFECGEVRVHPTGSVTVFTGSHSHGQGHETTFAQVVAARLGIPVENVDIVHGDTGRVP 547

Query: 516 GSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSKK 575
              GTYGSRS+++GG+A +K  +++  K K+ AA    A   +I +   EF+V+    KK
Sbjct: 548 FGMGTYGSRSISVGGAAIMKALDKIEAKAKKIAAHLMEASDADIDFSGGEFTVRG-TDKK 606

Query: 576 ASWDEIASLATTK--------EP-IVEKIYYE-NDVTFPYGVHVAVVEVDD-LGMARVVE 624
             + ++A  A           EP + E  +Y+  + TFP G ++  VE+D   G  RV +
Sbjct: 607 IPFGQVALTAYVPHNYPLDKLEPGLNETAFYDPTNFTFPAGTYICEVEIDPATGSTRVDK 666

Query: 625 YRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAIIN-ENGQ-LSVTYADYYVPTAVE 682
           + A DD G +INP + E Q+HGG VQG+GQA+ E  + + E GQ L+ ++ DY +P A +
Sbjct: 667 FTAVDDFGTIINPMIVEGQVHGGLVQGIGQAVLENCVYDRETGQLLTGSFMDYAMPRADD 726

Query: 683 APRF-ISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPE 738
            P F + +       ++ P GTKG GEA  I  P A+I A+ DA   +G +    P  P 
Sbjct: 727 FPEFKLGHVCTPC--THNPLGTKGCGEAGAIGSPPAVINAVLDALRPLGVKDFDMPASPH 784

Query: 739 EIYKAIMSKK 748
            +++AI S K
Sbjct: 785 RVWEAIQSAK 794


Lambda     K      H
   0.317    0.136    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: 1355
Number of extensions: 73
Number of successful extensions: 13
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: 748
Length of database: 795
Length adjustment: 41
Effective length of query: 707
Effective length of database: 754
Effective search space:   533078
Effective search space used:   533078
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: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources