GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mctC in Pseudomonas fluorescens FW300-N2C3

Align Monocarboxylic acid transporter (characterized)
to candidate AO356_19665 AO356_19665 cation/acetate symporter ActP

Query= SwissProt::Q8NS49
         (551 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_19665 AO356_19665
           cation/acetate symporter ActP
          Length = 552

 Score =  432 bits (1112), Expect = e-125
 Identities = 248/557 (44%), Positives = 340/557 (61%), Gaps = 37/557 (6%)

Query: 8   AQDAVSEGVGNPILNIS---VFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGL 64
           A DA++  V    LN++   +FV F+  T+ +     K  + + D+Y  G   +G QNGL
Sbjct: 20  AADALTGAVQKQPLNVAAILMFVAFVGATLYITYWASKKNNSAADYYAAGGKITGFQNGL 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  +A G+L V  FYLIAQM GAG L+ +L  LD H      V V +VGI+
Sbjct: 140 SYRLGQTQIRTLSASGSLVVVAFYLIAQMVGAGKLIQLLFGLDYH------VAVILVGIL 193

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

Query: 243 ATKGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKS 302
                    I+ PG      +   +   SL LAL  GTAGLPH+LMRF+TV  AKEARKS
Sbjct: 252 --------AIMSPG----GLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKS 299

Query: 303 VTWAIVLIGAFYLMTLVLGYGAAALVGP-----DRVIAAPGAANAAAPLLAFELGGSIFM 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 IGLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMIGGWLGLVSAVGLM 479

Query: 478 FLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKP---DNMDDLAAE 534
            L P +       + G + AIFP + P L S+ +AF+  W  ++  K     N   L   
Sbjct: 480 ILGPTI----WVQIMGHEKAIFPYEYPALFSMAIAFVGIWFFSITDKSAEGANERALFFP 535

Query: 535 MEVRSLTGVGVEKAVDH 551
             VRS TG+G   AV+H
Sbjct: 536 QFVRSQTGLGASGAVNH 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: 704
Number of extensions: 32
Number of successful extensions: 7
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.

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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