GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421 Acetate
           permease ActP (cation/acetate symporter)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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