GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Magnetospirillum magneticum AMB-1

Align Monocarboxylic acid transporter (characterized)
to candidate WP_011383956.1 AMB_RS07815 cation acetate symporter

Query= SwissProt::Q8NS49
         (551 letters)



>NCBI__GCF_000009985.1:WP_011383956.1
          Length = 561

 Score =  406 bits (1044), Expect = e-117
 Identities = 229/543 (42%), Positives = 325/543 (59%), Gaps = 39/543 (7%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I +FV+F+  T+ +       T  + DFY  G   +G QNGLAIAGDY+SAASFLGI   
Sbjct: 44  IIMFVIFVGATLGITYWAAGRTKTAADFYAAGGGITGFQNGLAIAGDYMSAASFLGISAL 103

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +  +GYDG ++S+G+ V W + L L+AE LRN+G++T ADV  +RL + P+R  AA G+L
Sbjct: 104 VYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKYTFADVCGYRLARTPIRTFAATGSL 163

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V +FYLI QM GAG L+ +L  +         V IVG +M+ YV  GGM  TT+VQ+IK
Sbjct: 164 IVVIFYLIGQMVGAGQLIKLLFGMD----YVYAVMIVGALMMVYVTFGGMVATTWVQIIK 219

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           A LL+GG   +      +       L   A+E H               I+ P    GA 
Sbjct: 220 ACLLLGGATFIAFGVMSQFGFSFEKLFVKAIEVHPKK----------VAIMAP----GAL 265

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
           +T  +D ISL +AL  GTAGLPH+LMRF+TVP A+EARKSV +A   IG FY++T ++G+
Sbjct: 266 VTNPVDAISLGMALMFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYILTFIIGF 325

Query: 323 GAAALV--GPDRV------IAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAG 374
           GA  +V   P+ +      +   G  N AA  LA  +GG++F+  ISAVAFAT+LAVV+G
Sbjct: 326 GAITMVATNPEYLTKGLGSLDLKGGNNMAAVWLAHAIGGNLFLGFISAVAFATILAVVSG 385

Query: 375 LAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVA 434
           L +  ++A+ HD+Y +VI +GQ+TE ++V VS+I  + +G+I+++LG++   QNVAF+VA
Sbjct: 386 LTLAGASAISHDLYASVIMHGQATEGKEVTVSKIASICLGVIAVLLGLVFEKQNVAFIVA 445

Query: 435 LAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGA 494
           L F+VAASAN P ++ S++W    T GAV     GL+ +++++ LS AV         G 
Sbjct: 446 LTFSVAASANFPVLVLSMFWGGLTTRGAVLGGMIGLLMSVIMVVLSKAVWVQSF----GF 501

Query: 495 DWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE------MEVRSLTGVGVEKA 548
              IFP   P L S+P AF   W+ +++   DN     AE        +RS TG+G E A
Sbjct: 502 KAEIFPFAYPALFSVPAAFFFSWLFSIM---DNSPSAQAERAAYEAQSIRSETGLGAEGA 558

Query: 549 VDH 551
             H
Sbjct: 559 ASH 561


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: 704
Number of extensions: 32
Number of successful extensions: 6
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: 551
Length of database: 561
Length adjustment: 36
Effective length of query: 515
Effective length of database: 525
Effective search space:   270375
Effective search space used:   270375
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