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 Sep 17 2021. 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