Alignments for a candidate for aldox-large in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Cupriavidus basilensis 4G11

Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate RR42_RS02365 RR42_RS02365 carbon monoxide dehydrogenase

Query= SwissProt::Q4J6M3
         (748 letters)



>FitnessBrowser__Cup4G11:RR42_RS02365
          Length = 793

 Score =  469 bits (1208), Expect = e-136
 Identities = 287/780 (36%), Positives = 431/780 (55%), Gaps = 44/780 (5%)

Query: 5   GKSIKRLNDDKFITGRSNYIDDIKIPSL-YAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63
           G S+KR  D +F+TG   Y DDI +P   Y  F+RSP+ HA I  ID T+AL   G+VA+
Sbjct: 11  GASVKRKEDYRFLTGNGQYTDDIVLPQQSYGYFLRSPHAHARIVSIDKTEALASPGVVAI 70

Query: 64  FSGKDINPMLKGGV--GVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQDKYAV 121
           F+G D+     GG+  G L   ++ S  +        +  K ++VG+ VA+VI +     
Sbjct: 71  FTGDDVAADKVGGLPCGWLIHSIDGSPMKEPAHPVLAQ-GKARHVGDQVALVIAETLQQA 129

Query: 122 RDAIDRVNVEYEQLKPVIKMEDAEKDEVIVHDELKTNVSYKIPFKAGD---IEKAFSQAD 178
           +DA ++++V+Y++L  V+    A     +VHD++  N SY   +  GD    + AF++A 
Sbjct: 130 KDAAEKIDVQYDELPAVVNTAHAASATSLVHDDVPENTSYV--WGHGDRAATDAAFAKAA 187

Query: 179 KVVKVEAINERLIPNPMEPRGILSVY--DGNSLSVWYSTQVPHFARSEF-ARIFGIPETK 235
            V  +E IN RLIPN +EPR + + Y    +S +V+ S Q PH  R    A + G+PE++
Sbjct: 188 HVTTLEIINNRLIPNAIEPRAVNASYTRQDDSYTVYVSNQNPHVERLLMGAFVLGLPESR 247

Query: 236 IRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARSNVFTGE 294
           +R+  PDVGG FGSK+ + AE++A+  +S  ++RP++WTA RSE  L  +  R +V   E
Sbjct: 248 LRIIAPDVGGGFGSKIFLYAEDVALTWASKKIKRPIKWTAERSESFLTDAHGRDHVTKAE 307

Query: 295 VAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIESTAVYTTT 353
           +A+  DG  L ++     ++GAYL+  A   PTI+   ++ G Y    +  E  AV+T T
Sbjct: 308 LAMDADGKFLAMRVHTTANMGAYLSTFASSVPTILYATLLAGQYATPAIYAEVRAVFTNT 367

Query: 354 PPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLRYDTGDY 413
            P+  YRGA RPEATY++ER++   A E+ +D   IR +N I   PY  P GL YDTGDY
Sbjct: 368 APVDAYRGAGRPEATYVVERLVEAAAREMKMDPAQIRRKNFIHDFPYATPVGLTYDTGDY 427

Query: 414 IRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP-------------WE 460
                      +        ++ + +G   G+G + Y+E C   P             +E
Sbjct: 428 EPCLARAQELADVKGFPARREEAKQRGKLRGLGYSCYIEACGLAPSNIAGALGARAGLFE 487

Query: 461 YGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVEGSFGT 520
            GEI+V   G V V TG+  HGQG ET  AQIVAD L I ++ + VV GDT  V    GT
Sbjct: 488 VGEIRVHPTGTVTVFTGSHSHGQGHETTFAQIVADRLGIALDAVEVVHGDTGRVPFGMGT 547

Query: 521 YGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSKKASWDE 580
           YGSRSL++GGSA +K  +++  K K+ AA    A   +I ++N  FSV      K ++ E
Sbjct: 548 YGSRSLSVGGSAIMKALDKIEAKAKKIAAHLLEASDADIEFKNGTFSVAGTDRSK-TFGE 606

Query: 581 IASLATTK--------EP-IVEKIYYE-NDVTFPYGVHVAVVEVD-DLGMARVVEYRAYD 629
           +A  A           EP + E  +Y+  + T+P G ++  VEVD D G ++V+++ A D
Sbjct: 607 VALTAYVPHNYPLDKLEPGLNENAFYDPTNFTYPSGAYICEVEVDPDTGESKVIKFTAVD 666

Query: 630 DIGKVINPALAEAQIHGGGVQGVGQALYEKAII-NENGQ-LSVTYADYYVPTAVEAPRFI 687
           D G +INP + E Q+HGG  QG+GQA+ E+ +  +++GQ L+ +Y DY +P A + P F 
Sbjct: 667 DFGNIINPMIVEGQVHGGIGQGLGQAMLEQCVYDDDSGQLLTGSYMDYAMPRAGDLPDFT 726

Query: 688 SYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPEEIYKAI 744
              A  +  ++ P G KG GEA  I  P A I A+ DA   +G    + P  P  +++ I
Sbjct: 727 VETAKGTPCTHNPLGVKGCGEAGAIGSPPAFINALVDALSPLGVHDIQMPATPHRVWQDI 786


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: 1451
Number of extensions: 73
Number of successful extensions: 12
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: 793
Length adjustment: 41
Effective length of query: 707
Effective length of database: 752
Effective search space:   531664
Effective search space used:   531664
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