GapMind for catabolism of small carbon sources

 

Aligments for a candidate for citW in Pseudomonas stutzeri RCH2

Align Electrogenic citrate:L-lactate exchanger, CitP or CitN (characterized)
to candidate GFF3854 Psest_3924 Na+/citrate symporter

Query= TCDB::P21608
         (442 letters)



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

 Score =  270 bits (691), Expect = 5e-77
 Identities = 151/414 (36%), Positives = 243/414 (58%), Gaps = 5/414 (1%)

Query: 26  RISGIGLIAYAFMAVLLIIAISTKTLPNTMIGAIFALVLMGHVFYYLGAHLPIFRSYLGG 85
           RI  + L  +A   +++  AI T TLP  MIGA+  ++L+G +  + G  LPI R+YLGG
Sbjct: 23  RIFNLPLPLFAIALLVMAAAIVTDTLPTGMIGALLVMMLLGELLGFAGDRLPIIRTYLGG 82

Query: 86  GSVFTILLTAILVATNVIPKYVVTTASGFINGMDFLGLYIVSLIASSLFKMDRKMLLKAA 145
           G++  +   A +V    +P  V    + F+ G  FL  YI +LI  S+  MD K+L+K  
Sbjct: 83  GAIMALFGAASMVYFGWLPAAVADDVASFMKGGGFLDFYIAALITGSILGMDAKVLVKVG 142

Query: 146 VRFLPVAFISMALTAVVIGIVGVIIGVGFNYAILYIAMPIMAGGVGAGIVPLSGIYAHAM 205
            R+      S+   A+    VG ++G     A++ IAMPIM GG+GAG VP+S IY   +
Sbjct: 143 SRYALPLLCSVLFAALFAMAVGALLGFSPQDAVVVIAMPIMGGGMGAGAVPMSQIYEQLL 202

Query: 206 GVGSAGILSKLFPTVILGNLLAIISAGLISRIFKDSKG-NGHGEILRGEREKSAAAEEIK 264
           G  ++  +S L P + LGN+ AII AGL++ +        G+G+++ G            
Sbjct: 203 GQPASYYISILVPALALGNVFAIIIAGLLNGLGNRYPSLTGNGQMMPGVDVSDKEGPITL 262

Query: 265 PDYVQLGVGLIIAVMFFMIGTMLNKVFPGINAYAFIILSIVLTKAFGLLPKYYEDSVIMF 324
           P    LG+GL+ A+ FF+ G +L K  P ++ YA +I+ + L K   L+P+   D+   +
Sbjct: 263 P---ALGIGLVAALSFFIAGQILGKFVP-LHPYALMIVLVALLKVSNLVPESINDAASQW 318

Query: 325 GQVIVKNMTHALLAGVGLSLLDMHVLLAALSWQFVVLCLVSIVAISLISATLGKLFGLYP 384
            + + +N T ALL G+G++  D+  +L A+S  +V++    +   +  +  +G+L G YP
Sbjct: 319 FRFVARNWTFALLFGIGVAFTDLGQVLDAISLTYVLIVFAVVAGAAFGAGLVGRLVGFYP 378

Query: 385 VEAAITAGLANNSMGGTGNVAVLAASERMNLIAFAQMGNRIGGALILVVAGILV 438
           +E+AITAGL   +MGGTG+VAVL+A+ RM+L+ FAQ+ +R+GGALIL+++ ++V
Sbjct: 379 IESAITAGLCMANMGGTGDVAVLSAARRMSLMPFAQISSRLGGALILLISSVVV 432


Lambda     K      H
   0.328    0.144    0.407 

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: 620
Number of extensions: 38
Number of successful extensions: 3
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: 442
Length of database: 437
Length adjustment: 32
Effective length of query: 410
Effective length of database: 405
Effective search space:   166050
Effective search space used:   166050
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