GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citA in Pseudomonas fluorescens FW300-N2E3

Align citrate transporter (characterized)
to candidate AO353_00400 AO353_00400 citrate-proton symporter

Query= CharProtDB::CH_014606
         (431 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_00400 AO353_00400
           citrate-proton symporter
          Length = 433

 Score =  534 bits (1376), Expect = e-156
 Identities = 254/412 (61%), Positives = 324/412 (78%)

Query: 6   SRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIAKTFFPAESEFAALMLTFAVFGSGFLM 65
           S  G   AI RV SGNFLE FDF ++GFYAT IAKTFFPA+S FA+LML+ A FG+GFLM
Sbjct: 3   STTGKGKAIFRVVSGNFLEMFDFMVYGFYATAIAKTFFPADSAFASLMLSLATFGAGFLM 62

Query: 66  RPIGAVVLGAYIDRIGRRKGLMITLAIMGCGTLLIALVPGYQTIGLLAPVLVLVGRLLQG 125
           RP+GA+ LGAYIDR GRRKGL+ITLA+M  GT+LIA VPGY T+G+ AP++VL GRLLQG
Sbjct: 63  RPLGAIFLGAYIDRHGRRKGLIITLALMAAGTVLIACVPGYATLGVAAPLIVLFGRLLQG 122

Query: 126 FSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYGLNVTLGHDEISEW 185
           FSAGVELGGVSVYL+EI+TPG KGF+ SWQSASQQ A+V A L+G GLN  L  +++ +W
Sbjct: 123 FSAGVELGGVSVYLAEISTPGRKGFFVSWQSASQQAAVVFAGLLGVGLNHWLSPEQMGDW 182

Query: 186 GWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREIFTTIAKNWRIITAGTLLVA 245
           GWR+PF +GCMI+P IF++RRSL+ET  F  RKHRP  R+I  +I++N+ I+ AG  LV 
Sbjct: 183 GWRVPFLVGCMIVPAIFIIRRSLEETPEFQARKHRPSLRDIVRSISQNFGIVLAGMALVV 242

Query: 246 MTTTTFYFITVYTPTYGRTVLNLSARDSLVVTMLVGISNFIWLPIGGAISDRIGRRPVLM 305
           MTT +FY IT YTPT+G+  L+LS  D+L+VT+ +G+SNF WLP+ GA+SD+IGR+P+L+
Sbjct: 243 MTTVSFYLITAYTPTFGKAELHLSDFDALLVTVCIGLSNFFWLPVMGALSDKIGRKPLLL 302

Query: 306 GITLLALVTTLPVMNWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMPVYVRTVG 365
             T+LA++T  P ++WL A P F+ + +V LW SF +G YNGAMV ALTE+MP+ VRT G
Sbjct: 303 AATILAILTAYPALSWLVANPSFSHLLIVELWLSFLYGSYNGAMVVALTEIMPIEVRTTG 362

Query: 366 FSLAFSLATAIFGGLTPAISTALVQLTGDKSSPGWWLMCAALCGLAATTMLF 417
           FSLA+SLATA FGG TPA  T L+ +  +K++PG WL  AA+ GL AT +LF
Sbjct: 363 FSLAYSLATATFGGFTPAACTYLIHVLDNKAAPGIWLSGAAVLGLIATLVLF 414


Lambda     K      H
   0.328    0.141    0.432 

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: 605
Number of extensions: 17
Number of successful extensions: 1
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: 431
Length of database: 433
Length adjustment: 32
Effective length of query: 399
Effective length of database: 401
Effective search space:   159999
Effective search space used:   159999
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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 preprint 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