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_4275 Acetate permease ActP (cation/acetate symporter)

Query= SwissProt::Q8NS49
         (551 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4275
          Length = 552

 Score =  438 bits (1127), Expect = e-127
 Identities = 250/557 (44%), Positives = 343/557 (61%), Gaps = 37/557 (6%)

Query: 8   AQDAVSEGVGNPILNIS---VFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGL 64
           A DA++  V    LN+S   +FV F+  T+ +     K  + + D+Y  G   +G QNGL
Sbjct: 20  AADALTGAVQKQPLNVSAIVMFVAFVGATLCITYWASKRNNSAADYYAAGGKITGFQNGL 79

Query: 65  AIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVL 124
           AIAGDY+SAASFLGI   +  +GYDG +YSIGF V W + L L+AE LRN+G++T ADV 
Sbjct: 80  AIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIILFLIAERLRNLGKYTFADVA 139

Query: 125 SFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVL--LDIHEFKWQAVVVGIVGIV 182
           S+RL Q  +R  +ACG+L V  FYLIAQM GAG L+ +L  LD H      V V +VGI+
Sbjct: 140 SYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYH------VAVILVGIL 193

Query: 183 MIAYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYA 242
           M  YVL GGM  TT+VQ+IKAVLL+ G + M ++    V+     L ++A++ H  +D  
Sbjct: 194 MCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNMLFSEAIKVHPKAD-- 251

Query: 243 ATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKS 302
                    I+ P    G  +   +   SL LAL  GTAGLPH+LMRF+TV  AKEARKS
Sbjct: 252 --------AIMSP----GGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKS 299

Query: 303 VTWAIVLIGAFYLMTLVLGYGAAALVG-----PDRVIAAPGAANAAAPLLAFELGGSIFM 357
           V +A   IG FY++T ++G+GA  LV       D   A  G  N AA  LA  +GGSIF+
Sbjct: 300 VLYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALLGGNNMAAVHLANAVGGSIFL 359

Query: 358 ALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLIS 417
             ISAVAFAT+LAVVAGL +  ++AV HD+Y +VI+ G++ E +++RVS+IT + + +++
Sbjct: 360 GFISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVLA 419

Query: 418 IVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLI 477
           I LGIL  +QN+AF+V LAF++AAS N P +L S+YWKK  T GA+   + GL+SA+ L+
Sbjct: 420 IGLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMIGGWMGLVSAVGLM 479

Query: 478 FLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGK---PDNMDDLAAE 534
            L P +       +   + AIFP + P L S+ +AF+  W  ++  K    DN   L   
Sbjct: 480 VLGPTI----WVQILHHEKAIFPYEYPALFSMMIAFVGIWFFSVTDKSTAADNERALFFP 535

Query: 535 MEVRSLTGVGVEKAVDH 551
             VRS TG+G   AV H
Sbjct: 536 QFVRSQTGLGASGAVSH 552


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: 696
Number of extensions: 34
Number of successful extensions: 8
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: 552
Length adjustment: 36
Effective length of query: 515
Effective length of database: 516
Effective search space:   265740
Effective search space used:   265740
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.

Links

Downloads

Related tools

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