GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc03102
          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:

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