GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF3786 Psest_3855 Branched-chain amino
           acid ABC-type transport system, permease components
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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