GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mctC in Pseudomonas fluorescens GW456-L13

Align Monocarboxylic acid transporter (characterized)
to candidate PfGW456L13_2421 Acetate permease ActP (cation/acetate symporter)

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421
          Length = 548

 Score =  431 bits (1108), Expect = e-125
 Identities = 244/540 (45%), Positives = 332/540 (61%), Gaps = 36/540 (6%)

Query: 23  ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82
           I +F+VF++ T+ V       T  ++DFYT G   +G QNGLAIAGD +SAASFLGI   
Sbjct: 34  IGMFLVFVLFTLGVTRWAALRTRSTSDFYTAGGGMTGFQNGLAIAGDMISAASFLGISAM 93

Query: 83  ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142
           + LNGYDG LY++G    W + L L+AE LRN+G++T ADV+S+RL Q PVR+ +A GTL
Sbjct: 94  MFLNGYDGLLYALGVLAGWPIILFLIAERLRNLGKYTFADVVSYRLEQTPVRLTSAFGTL 153

Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202
            V L YL+AQM GAG L+ +L  I         V +VG++M+ YV  GGM  TT+VQ+IK
Sbjct: 154 TVALMYLVAQMVGAGKLIELLFGID----YLYAVMLVGVLMVFYVTFGGMLATTWVQIIK 209

Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262
           AV+L+ G + M  +           +   A   HA       KG     I+ P    G  
Sbjct: 210 AVMLLFGTSFMAFMVLKHFGFSTEAMFAGATAVHA-------KG---NAIMAP----GGL 255

Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVLGY 322
           L+  +D ISL L +  GTAGLPH+LMRF+TV  AKEARKSV +A   IG FYL+ +++G+
Sbjct: 256 LSNPIDAISLGLGMMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYLLLIIVGF 315

Query: 323 GAAALVGPDRVI-----AAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377
           GA  +VG D        A  G  N  A  LA  +GG++F+  ISAVAFAT+LAVVAGLA+
Sbjct: 316 GAIVMVGTDPAFRDASGAIIGGGNMVAVHLAHAVGGNLFLGFISAVAFATILAVVAGLAL 375

Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437
           + ++AV HD+Y  V+R GQ++E +++RVSRI  + IG+++IVLG+L  +QN+AFL  L  
Sbjct: 376 SGASAVSHDLYACVMRKGQASEQQEMRVSRIATLCIGVLAIVLGLLFESQNIAFLSGLVL 435

Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWA 497
           A+AAS N P +  S+YWK   T GAV    +GL+SA++L+ LSPAV  N    V   D A
Sbjct: 436 AIAASVNFPVLFLSMYWKGLTTRGAVLGSLSGLVSAIVLLVLSPAVWVN----VMHHDKA 491

Query: 498 IFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAE------MEVRSLTGVGVEKAVDH 551
           +FP  NP L S+ LAF + W+ ++    D     A E        +RS+TG+G   A  H
Sbjct: 492 LFPYSNPALFSMSLAFFSAWLFSVT---DTSPRAALERGRYLAQFIRSMTGIGATGASKH 548


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: 684
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: 548
Length adjustment: 36
Effective length of query: 515
Effective length of database: 512
Effective search space:   263680
Effective search space used:   263680
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