GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudomonas stutzeri RCH2

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__psRCH2:GFF3786
          Length = 295

 Score =  177 bits (448), Expect = 3e-49
 Identities = 101/285 (35%), Positives = 173/285 (60%), Gaps = 5/285 (1%)

Query: 5   LQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFFVA 64
           L QL+ GLI GS YA+L+LG  +++G++K+INFAHG  YM+GAF GY L+ +  + ++ A
Sbjct: 13  LGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYLLLATLGIGYWPA 72

Query: 65  LIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTR--AFP 122
           LI+A +   +   VIE LA   L +   +  L+   G++  LE    Y  G++ +  A P
Sbjct: 73  LILAPIIVGLCSAVIERLALSRLYNLDHLYSLLFTFGLALALEGAFRYFYGSSGQPYAVP 132

Query: 123 QAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQLMG 182
           + +    Y+LG + L   +  ++  SL++ I   ++++KTK+G  +RA + +    +  G
Sbjct: 133 KEL-AGGYNLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGAYLRAATENPTLVRTFG 191

Query: 183 INVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPGAA 242
           INV   ++FT+ +G+ALAG AG+L A  Y  + PLMG    +  F   V+GG+G I GA 
Sbjct: 192 INVPLLLTFTYGMGAALAGLAGMLAAPIY-QVSPLMGSNLIIVVFAVVVVGGMGSILGAI 250

Query: 243 LGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGKN 287
           + G+++G+LE     F   +  + +++ I+ ++L+VRPAG++G++
Sbjct: 251 ITGYMLGILEGLTKVF-YPEASNIVIFVIMAIVLLVRPAGLMGRD 294


Lambda     K      H
   0.330    0.146    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: 247
Number of extensions: 14
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
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: 48 (23.1 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:

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