Alignments for a candidate for mctC in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctC in Dechlorosoma suillum PS

Align Monocarboxylic acid transporter (characterized)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__PS:Dsui_0290
          Length = 582

 Score =  426 bits (1096), Expect = e-124
 Identities = 245/555 (44%), Positives = 331/555 (59%), Gaps = 37/555 (6%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I +F  F++ T+ +       T  + DFYT G   +G QNGLAIAGDY+SAASFLGI  A
Sbjct: 39  IIMFGAFVLATLWITKWAASKTKTAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAA 98

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           +  NGYDG +YSIGF V W + + L+AE LRN+G+FT ADV ++R +  P+R  AA GTL
Sbjct: 99  VFANGYDGLIYSIGFLVGWPIIMFLMAERLRNLGKFTFADVAAYRFQATPIRALAASGTL 158

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V  FYLIAQM GAG L+ +L  +    W AVV  +VGI+M+ YVL GGM  TT+VQ+IK
Sbjct: 159 VVVAFYLIAQMVGAGQLIKLLFGLD--YWMAVV--LVGILMMVYVLFGGMTATTWVQIIK 214

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVE------------KHAASDYAATKGYDPT 250
           AVLL+ G + M  +   K       L  DAV             K   +D +AT      
Sbjct: 215 AVLLLSGASFMVFMVLAKYGFSPEALFADAVRIKTDLAAKGLLAKALETDPSATAETVAA 274

Query: 251 QILEPG---LQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAI 307
                G   +  G+ +   +  IS  +AL  GTAGLPH+LMRF+TVP  KEARKSV WA 
Sbjct: 275 AAAAKGQSIMGPGSFIKDPISAISFGMALMFGTAGLPHILMRFFTVPDGKEARKSVFWAT 334

Query: 308 VLIGAFYLMTLVLGYGAAALVGP-----DRVIAAPGAANAAAPLLAFELGGSIFMALISA 362
             IG FY++T ++G+GA  LVG      D      G  N AA  LA  +GG++F+  ISA
Sbjct: 335 TWIGYFYILTFIIGFGAIVLVGTNPEFLDAKGVLKGGGNMAAIHLANAVGGNVFLGFISA 394

Query: 363 VAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGI 422
           VAFAT+LAVVAGL ++ ++AV HD+Y +V R+G    A ++RVS++T V +G+I++VLGI
Sbjct: 395 VAFATILAVVAGLTLSGASAVSHDLYASVFRHGNVDSATEMRVSKMTTVALGIIAVVLGI 454

Query: 423 LAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPA 482
               QN+AF+V+LAFA+AASAN P +  S+ WK   T GA    + GLI+A++L  LS +
Sbjct: 455 AFEKQNIAFMVSLAFAIAASANFPVLFMSVLWKDCTTKGAFYGGFLGLITAVVLTVLSKS 514

Query: 483 VSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE------ME 536
           +  +    + G    IFP  +P L S+   FI  W+ +L+   D  +  A E       E
Sbjct: 515 IWVD----ILGNKTEIFPYASPALFSMAAGFIGIWLFSLM---DRSEQAAKERVAYLDQE 567

Query: 537 VRSLTGVGVEKAVDH 551
           +RS TG+G   A  H
Sbjct: 568 IRSETGIGAAAASSH 582



 Score = 29.3 bits (64), Expect = 4e-04
 Identities = 56/237 (23%), Positives = 94/237 (39%), Gaps = 32/237 (13%)

Query: 278 LGTAGLPHVLMRFYTVPTAKEARKSVT-W-AIVLIGAFYLMTLVLGYGAAALVGPDRVIA 335
           L  AGL  +    +      +A K  T W AI++ GAF L TL +   AA+     +   
Sbjct: 8   LALAGLGLLSSPVFAAALEGQAEKQATNWTAIIMFGAFVLATLWITKWAAS-----KTKT 62

Query: 336 APGAANAAAPLLAFELGGSIFMALISAVAFATVLAVV-----AGLAITASAAVGHDIYNA 390
           A     A   +  F+ G +I    +SA +F  + A V      GL  +    VG  I   
Sbjct: 63  AADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFANGYDGLIYSIGFLVGWPIIMF 122

Query: 391 VIRNGQSTEAEQVR-VSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVAA----SANL 445
           ++       AE++R + + T   +         +        LV +AF + A    +  L
Sbjct: 123 LM-------AERLRNLGKFTFADVAAYRFQATPIRALAASGTLVVVAFYLIAQMVGAGQL 175

Query: 446 PTILYSL-YWKKFNTTGAVAAIYT--GLISALLLIFLSPAVSGNDSAMVPGADWAIF 499
             +L+ L YW      G +  +Y   G ++A   + +  AV      ++ GA + +F
Sbjct: 176 IKLLFGLDYWMAVVLVGILMMVYVLFGGMTATTWVQIIKAV-----LLLSGASFMVF 227


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: 710
Number of extensions: 34
Number of successful extensions: 7
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: 582
Length adjustment: 36
Effective length of query: 515
Effective length of database: 546
Effective search space:   281190
Effective search space used:   281190
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources