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_0522 Dsui_0522 SSS sodium solute transporter

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__PS:Dsui_0522
          Length = 557

 Score =  410 bits (1055), Expect = e-119
 Identities = 245/570 (42%), Positives = 331/570 (58%), Gaps = 48/570 (8%)

Query: 5   ILLAQDAVSEGVGNP---------ILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGA 55
           +LLA  A   G G           +  I++FV F++ T+ +       T  + DFYT G 
Sbjct: 13  LLLAAGAAYAGPGTVGEAEKQPLNVAAIAMFVAFVLSTLGITYWAANRTKSTADFYTAGG 72

Query: 56  SFSGTQNGLAIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNV 115
             +G QNGLAIAGDY+SAA+ LG+   +   GYDGF+Y +GFFV W + L L+AE LRN+
Sbjct: 73  GITGFQNGLAIAGDYMSAATLLGLTSMVFAKGYDGFVYIVGFFVGWPIILFLMAERLRNL 132

Query: 116 GRFTMADVLSFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVV 175
           GRFT AD+ S+RL Q  VR  AA  +L V LFYLI QM GAG L+ +L  +       V 
Sbjct: 133 GRFTFADITSYRLDQSKVRTVAAISSLTVVLFYLITQMVGAGQLIKLLFGLD----YEVA 188

Query: 176 VGIVGIVMIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEK 235
           V +VG++M+ YV  GGM  TT+VQ+IKA LL+GG  +M +L          TL+  A E 
Sbjct: 189 VVVVGVLMMVYVTFGGMIATTWVQIIKACLLLGGGTLMMLLAMSHFGFDFETLVTKATEV 248

Query: 236 HAASDYAATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPT 295
           H           D T+I+ P    G+ L   ++ +SL+L L  GTAGLPH+LMRF+TVP 
Sbjct: 249 HK----------DGTKIMGP----GSLLADPVNAVSLSLGLMFGTAGLPHILMRFFTVPD 294

Query: 296 AKEARKSVTWAIVLIGAFYLMTLVLGYGAAALVGPDRVI--------AAPGAANAAAPLL 347
           AK+ARKSV  A   IG F+L+ ++LG  A  LVG +              G  N  A  L
Sbjct: 295 AKQARKSVFVATGFIGFFFLVVVLLGMSAIVLVGTNPEFFEGGNVGGKMIGGGNMVAMHL 354

Query: 348 AFELGGSIFMALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSR 407
           A  +GG+IF+  +SAVAFAT+LAVV+GLA+  ++A+ HDIY  VI  G+     +++VS+
Sbjct: 355 AKFVGGNIFLGFLSAVAFATILAVVSGLALAGASAISHDIYANVICKGKPKGGSELKVSK 414

Query: 408 ITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIY 467
           I  + IGL +I LGI+   QN+AF+V LAF +AASAN P ++ S+YWK   T GA+A   
Sbjct: 415 IASIFIGLAAIGLGIMFEKQNLAFMVGLAFGIAASANFPVLILSMYWKGLTTKGAIAGTI 474

Query: 468 TGLISALLLIFLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDN 527
            GL +A++ + LS AV       V G   AIFP   P L S+PLAF+   I  +V K D 
Sbjct: 475 CGLTAAVVFVVLSKAV----WVTVLGKAQAIFPYDQPALFSMPLAFL---IAFVVSKLDT 527

Query: 528 MDDLAAEME------VRSLTGVGVEKAVDH 551
                 E+E      VR+ TG+G   A +H
Sbjct: 528 SAQAKREIEAFDDQYVRAQTGLGAAGASNH 557


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: 678
Number of extensions: 33
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: 557
Length adjustment: 36
Effective length of query: 515
Effective length of database: 521
Effective search space:   268315
Effective search space used:   268315
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