GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citS in Pseudomonas stutzeri RCH2

Align Citrate:Na+ symporter, CitS (characterized)
to candidate GFF3854 Psest_3924 Na+/citrate symporter

Query= TCDB::P31602
         (446 letters)



>lcl|FitnessBrowser__psRCH2:GFF3854 Psest_3924 Na+/citrate symporter
          Length = 437

 Score =  307 bits (786), Expect = 5e-88
 Identities = 162/424 (38%), Positives = 257/424 (60%), Gaps = 11/424 (2%)

Query: 18  LLGFKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAIFGEIGKRLPIFNK 77
           LL  +IF +PLPL+A AL+ +  +   + LPT ++G   +M ++G + G  G RLPI   
Sbjct: 19  LLSQRIFNLPLPLFAIALLVMAAAIVTDTLPTGMIGALLVMMLLGELLGFAGDRLPIIRT 78

Query: 78  YIGGAPVMIFLVAAYFVYAGIFTQKEIDAISNVMDKSNFLNLFIAVLITGAILSVNRRLL 137
           Y+GG  +M    AA  VY G       D +++ M    FL+ +IA LITG+IL ++ ++L
Sbjct: 79  YLGGGAIMALFGAASMVYFGWLPAAVADDVASFMKGGGFLDFYIAALITGSILGMDAKVL 138

Query: 138 LKSLLGYIPTILMGIVGASIFGIAIGLVFGIPVDRIMMLYVLPIMGGGNGAGAVPLSEIY 197
           +K    Y   +L  ++ A++F +A+G + G      +++  +PIMGGG GAGAVP+S+IY
Sbjct: 139 VKVGSRYALPLLCSVLFAALFAMAVGALLGFSPQDAVVVIAMPIMGGGMGAGAVPMSQIY 198

Query: 198 HSVTGRSREEYYSTAIAILTIANIFAIVFAAVLDIIGKKHTWLSGEGELVRKASFKVEED 257
             + G+    Y S  +  L + N+FAI+ A +L+ +G ++  L+G G+++      V+  
Sbjct: 199 EQLLGQPASYYISILVPALALGNVFAIIIAGLLNGLGNRYPSLTGNGQMMP----GVDVS 254

Query: 258 EKTGQITHRETAVGLVLSTTCFLLAYVVAKKILPSIGGVAIHYFAWMVLIVAALNASGLC 317
           +K G IT     +GLV + + F+   ++ K        V +H +A M+++VA L  S L 
Sbjct: 255 DKEGPITLPALGIGLVAALSFFIAGQILGK-------FVPLHPYALMIVLVALLKVSNLV 307

Query: 318 SPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIINAITFANVVIAAIIVIGAVLGA 377
              I   A +   F ++   + L+ G+GV +TDL ++++AI+   V+I   +V GA  GA
Sbjct: 308 PESINDAASQWFRFVARNWTFALLFGIGVAFTDLGQVLDAISLTYVLIVFAVVAGAAFGA 367

Query: 378 AIGGWLMGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYAQISSRLGGGIVLVI 437
            + G L+GF+PIESAITAGLCMAN GG+GD+ VLSA  RM+L+ +AQISSRLGG ++L+I
Sbjct: 368 GLVGRLVGFYPIESAITAGLCMANMGGTGDVAVLSAARRMSLMPFAQISSRLGGALILLI 427

Query: 438 ASIV 441
           +S+V
Sbjct: 428 SSVV 431


Lambda     K      H
   0.327    0.144    0.420 

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: 588
Number of extensions: 27
Number of successful extensions: 4
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: 446
Length of database: 437
Length adjustment: 32
Effective length of query: 414
Effective length of database: 405
Effective search space:   167670
Effective search space used:   167670
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 (21.7 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