GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Shewanella oneidensis MR-1

Align Monocarboxylic acid transporter (characterized)
to candidate 201983 SO2857 sodium/solute symporter family protein (NCBI ptt file)

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__MR1:201983
          Length = 578

 Score =  171 bits (432), Expect = 9e-47
 Identities = 154/589 (26%), Positives = 256/589 (43%), Gaps = 80/589 (13%)

Query: 27  VVFIIVTMTVVLRVGKS----TSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           + ++IV ++  L +G +       + +FY  G       NG+A A D++SAASF+ + G 
Sbjct: 6   LTYLIVGLSFALYIGIALWTRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFISLAGI 65

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +S  GYDG +Y +G+   +++  L +A  LR  G+FT+ D L  R   +  R  A    +
Sbjct: 66  VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFLGERYYSQAARTVAVICAI 125

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            +   Y+  QM G G + S  L++       V +G+   V+  Y +LGGMKG TY Q+ +
Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVEVD--TGVYIGMA--VVFFYSVLGGMKGITYTQVAQ 181

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVE-KHAASDYAATKGYDPTQILEPGL---Q 258
             +L+    +  +   V ++G +   +    +   AA + +     D    L   L    
Sbjct: 182 YCVLIFAFMVPAIFLSVMMTGHIIPQIGFGAQLLDAAGNNSGVYLLDKLNNLSVDLGFAP 241

Query: 259 YGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTL 318
           Y     + +D + +  AL +GTAGLPHV++RF+TVP  K+AR S  WA+V I   Y  T 
Sbjct: 242 YTDGSKSMIDVLCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY--TT 299

Query: 319 VLGYGAAALV-------GPD-------------------------------RVIAAPGAA 340
           V    A + V       GPD                               ++  A G  
Sbjct: 300 VPALAAFSRVNMIETINGPDQKGVAYETAPNWIKNWEKTGLIKWDDKNGDGKIYYATGKI 359

Query: 341 NAAAPLLAFELGGSIF--------------MALISAVAFATVLAVVAGLAITASAAVGHD 386
             AA     ++   I               +AL++A   A  L+  AGL +  S +V HD
Sbjct: 360 EDAASTNEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHD 419

Query: 387 IYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQN--VAFLVALAFAVAASAN 444
           +    +    S + E +       +  G+  ++ G   +     VA +VA AF +AAS+ 
Sbjct: 420 LLKKNLMPNISDKKELMYAR----LAAGIGIVIAGYFGVNPPGFVAAVVAFAFGLAASSL 475

Query: 445 LPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWAI-FPLKN 503
            P I+  ++ K  N  GA+A +  GL      I     +  + +A VP A+W +    + 
Sbjct: 476 FPAIIMGIFSKTMNKEGAIAGMILGLFFTSGYIVYFKFI--DPTANVP-ANWFLGISPEG 532

Query: 504 PGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLT-GVGVEKAVDH 551
            G+V + + F+   +  +V K      +  +  V S+    G  +A DH
Sbjct: 533 IGMVGMVINFV---VAAIVSKVTAATPVHVQEMVESIRFPKGAGEASDH 578


Lambda     K      H
   0.324    0.138    0.393 

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: 643
Number of extensions: 32
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 551
Length of database: 578
Length adjustment: 36
Effective length of query: 515
Effective length of database: 542
Effective search space:   279130
Effective search space used:   279130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (25.0 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