GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldox-large in Sinorhizobium meliloti 1021

Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate SMc03102 SMc03102 carbon monoxide dehydrogenase large subunit transmembrane protein

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



>lcl|FitnessBrowser__Smeli:SMc03102 SMc03102 carbon monoxide
           dehydrogenase large subunit transmembrane protein
          Length = 781

 Score =  461 bits (1187), Expect = e-134
 Identities = 282/779 (36%), Positives = 418/779 (53%), Gaps = 40/779 (5%)

Query: 4   VGKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGIVA 62
           +G  V R  D +F+TG+  Y DD+ +P + YA FVRS + HA I+ ID + A  + G++ 
Sbjct: 6   IGARVARKEDKRFLTGKGRYTDDMVVPGMKYAVFVRSPHAHATIRSIDATSAKSMPGVID 65

Query: 63  VFTAKEINPLLKGGIRP----WPTYI-DIRSFRYSERKAFPENKVKYVGEPVAIVLGQDK 117
           V   K+   LL  GI      W  +  D    R    +      V+YVG+ VAIV+    
Sbjct: 66  VLDGKQ---LLADGIGNLICGWMIHSKDGSPMRMGAWRPLAHETVRYVGDAVAIVVADSV 122

Query: 118 YSVRDAIDKVVVEYEPLKPVIRMEEA-EKDQVIIHEELKTNISYKIPF-KAGEVDKAFSE 175
              RDA + VVV+YE L  V    +A  + +  IH E   N+ +      AG  D+A + 
Sbjct: 123 AQARDAAEAVVVDYETLPVVTETLQALGEGEPQIHPEAPGNLIFDWELGDAGAADQAIAA 182

Query: 176 SDKVVRVEAINERLIPNPMEPRGIVSRFEAGT--LSIWYSTQVPHYMRSEFARILGI-PE 232
           +  V  ++ IN RL PN MEPR  +  ++AG    + + ++Q PH  R   +    + PE
Sbjct: 183 AAHVTELKIINNRLSPNAMEPRATLGIYDAGDDHFTCYTTSQNPHLARLVMSAFYNVAPE 242

Query: 233 SKIKVSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFT 291
           +K++V  PDVGG FG+K+ + PEE+  + +S   G PV+WTA R+E  L  +  R +V T
Sbjct: 243 NKLRVIAPDVGGGFGSKIFIYPEEIVCLWASKRTGVPVKWTADRTEAFLTDAHGRDHVST 302

Query: 292 GEVAVKRDGTILGIKGKLLLDLGAYITVTAGIQPLII-PMMIPGPYKIRNLDIESVAVYT 350
            ++A      I  +K   + +LGAY+++ +   P  +   ++ G Y I  +      VYT
Sbjct: 303 VKMAFDSSNRITALKVDTIANLGAYMSLFSSCVPTYLYATLLSGQYAIPAIHANVRTVYT 362

Query: 351 NTPPITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTELPYTNPFGLRYDSG 410
           NT P+  YRGA RPEATY++ER + T A ELG+    +R  N +   P+  P  + YD+G
Sbjct: 363 NTAPVDAYRGAGRPEATYLLERTIETAARELGISPAELRRINFIRTFPHQTPVIMNYDAG 422

Query: 411 DYVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGP------------- 457
           DY   LR  ++   +        E  ++G + G+G++ Y+E C   P             
Sbjct: 423 DYEASLRGAMEAADWDGFAARKAEAERRGMKRGIGMSCYIEACGLAPSAAVGSLGAGVGL 482

Query: 458 WEYAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASM 517
           WE AEVRV+  G + V+TG+  HGQG ET  AQ+VA+   + I  V ++ GDTD V   M
Sbjct: 483 WESAEVRVNAVGTIEVMTGSHSHGQGHETTFAQVVAERFGVPIDSVNIVHGDTDKVQMGM 542

Query: 518 GTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSW 577
           GTYGSRS  +G SA  K  +K+  K KRIAA     D  ++  E G  K+     + + W
Sbjct: 543 GTYGSRSGAVGMSAVFKALDKVEAKAKRIAAHMMEADESDIVIEDGALKVAG-TDRSVPW 601

Query: 578 DDVASIAYRSH------DPGLVEKIIYE-NDVTFPYGVHIATVEVD-DTGVARVLEYRAY 629
             VA  +Y +H      +PGL E   Y+ ++ TFP G +I  VEVD +TG  +++++ A 
Sbjct: 602 SQVALASYTAHNLPPGMEPGLKEGAFYDPSNFTFPAGCYICEVEVDPETGRTKIVQFVAA 661

Query: 630 DDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVEAPKFT 688
           DD G ++NP + E Q+HGG  Q +GQAL E    +++GQL+  +Y DY +P A + P FT
Sbjct: 662 DDFGNIINPLIVEGQVHGGLAQGIGQALLEGVHYDQSGQLLTASYMDYAMPRADDLPSFT 721

Query: 689 SVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDAIGTRFTKTPTTPEEILRAIAS 747
              ++   PSN P G KG GEA  I  P  +I A+ DAIGT     P TP+++  A+ S
Sbjct: 722 VTTSNTPCPSN-PLGVKGCGEAGAIGSPPALINAITDAIGTNELTMPATPQKVWVAVHS 779


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: 1332
Number of extensions: 63
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: 781
Length adjustment: 40
Effective length of query: 709
Effective length of database: 741
Effective search space:   525369
Effective search space used:   525369
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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