Alignments for a candidate for aldox-large in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldox-large in Azospirillum brasilense Sp245

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate AZOBR_RS08560 AZOBR_RS08560 carbon-monoxide dehydrogenase

Query= metacyc::MONOMER-18071
         (749 letters)



>FitnessBrowser__azobra:AZOBR_RS08560
          Length = 796

 Score =  470 bits (1209), Expect = e-136
 Identities = 284/784 (36%), Positives = 433/784 (55%), Gaps = 46/784 (5%)

Query: 4   VGKPVKRIYDDKFVTGRSTYVDDIRIPA-LYAGFVRSTYPHAIIKRIDVSDALKVNGIVA 62
           +G  V+R  D +F+TGR TY DDI  P   +A FVRS Y HA I  ID ++A++  G++A
Sbjct: 7   IGASVRRREDARFLTGRGTYTDDINRPGQTHAVFVRSPYAHARITGIDAAEAMRAPGVIA 66

Query: 63  VFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFPE-----NKVKYVGEPVAIVLGQDK 117
           V T  ++     G +   P    I S   S  K  P      ++ +YVG+ VA+V+ + +
Sbjct: 67  VLTGADMEADKVGSL---PCGWQIHSKDGSPMKEPPHFPIARDRARYVGDAVAVVIAETR 123

Query: 118 YSVRDAIDKVVVEYEPLKPVIRMEEA-EKDQVIIHEELKTNISYKIPF-KAGEVDKAFSE 175
              +DA + V+V+YE L   +   +A E    ++H+++  N+ +      A  VD AFS+
Sbjct: 124 EQAKDAAELVMVDYEELPAAVTSLKALEGGAPLVHDDVGGNLCFDWHLGDAAAVDAAFSQ 183

Query: 176 SDKVVRVEAINERLIPNPMEPRGIVSRFE--AGTLSIWYSTQVPHYMRSEF-ARILGIPE 232
           +  V +++ +N+RL+PN MEPR  +  ++   G  ++  ++Q PH +R    A +LGIPE
Sbjct: 184 AAHVAKLDLVNQRLVPNAMEPRAALGEYDRATGEHTLTTTSQNPHVIRLLMGAFVLGIPE 243

Query: 233 SKIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFT 291
            K++V  PDVGG FG+K+    EE  V  ++  +GRPV+WTA RSE  L  +  R +V  
Sbjct: 244 HKLRVVAPDVGGGFGSKIFHYGEEAVVTWAAKKVGRPVKWTAERSESFLTDAHGRDHVSH 303

Query: 292 GEVAVKRDGTILGIKGKLLLDLGAYITVTA-GIQPLIIPMMIPGPYKIRNLDIESVAVYT 350
            E+A+ +DG  L ++   + ++GAY++  A  I   +   ++ G YK   +  E  AV+T
Sbjct: 304 AELAMDKDGNFLALRVATIANMGAYLSTFAPSIPTYLYATLLAGQYKTPAIYAEVKAVFT 363

Query: 351 NTPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLV--TELPYTNPFGLRYD 408
           NT P+  YRGA RPEA Y+IER++   A E G+D   +R +N V  + +PY  P  L+YD
Sbjct: 364 NTVPVDAYRGAGRPEACYLIERLVEVAAAETGIDKAELRRRNFVPASAMPYQTPVALQYD 423

Query: 409 SGDYVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP----------- 457
           +GD+   L   +  + Y        E  ++G   G+G A Y+E C   P           
Sbjct: 424 TGDFAKNLDIALPLVDYDGFAARKAESARRGKLRGIGFATYIEACGIAPSNVAGALGARA 483

Query: 458 --WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAA 515
             +E AEVR    G V V TG+  HGQG ET  AQ+V++   + I  V ++ GDT  +  
Sbjct: 484 GLYESAEVRFHPTGSVTVFTGSHSHGQGHETTFAQLVSERFGVPIENVEIVHGDTSKIPF 543

Query: 516 SMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKM 575
            MGTYGSRS+ +GGSA +K  +K+  K K+IAA        +++ + G F +     K +
Sbjct: 544 GMGTYGSRSLAVGGSAIVKAMDKVERKAKKIAAHMLEAAEADIEVKDGRFVVAG-TDKAL 602

Query: 576 SWDDVASIAYRSH-------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVLEY 626
           +  D+A  AY  H       +PGL E+  Y+  + T+P G H+  VE+D DTGV +V+ +
Sbjct: 603 TIGDIALQAYVPHNFPLDELEPGLDEQAFYDPKNFTYPNGCHVCEVEIDPDTGVVQVVNF 662

Query: 627 RAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNE-NGQLIV-TYADYYVPTAVEA 684
            A DD G+V+NP + E Q+HGG VQ +GQALYE  + +E +GQLI  +Y DY +P A + 
Sbjct: 663 AAVDDFGRVINPLIVEGQVHGGLVQGIGQALYENCVYDEDSGQLITGSYMDYCMPRADDV 722

Query: 685 PKFTSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAI---GTRFTKTPTTPEEI 741
           P FT  + +    ++ P G KG GEA  I   A ++ A+  A+   G      P TPE +
Sbjct: 723 PSFTVRYHEDQPCTHNPLGVKGCGEAGTIGASAAVMNAVVHALSEYGVTHLDMPATPERV 782

Query: 742 LRAI 745
            +AI
Sbjct: 783 WQAI 786


Lambda     K      H
   0.317    0.136    0.394 

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: 1472
Number of extensions: 68
Number of successful extensions: 11
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: 749
Length of database: 796
Length adjustment: 41
Effective length of query: 708
Effective length of database: 755
Effective search space:   534540
Effective search space used:   534540
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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