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 GFF1059 Psest_1092 Branched-chain amino acid ABC-type transport system, permease components

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__psRCH2:GFF1059
          Length = 295

 Score =  162 bits (410), Expect = 8e-45
 Identities = 92/293 (31%), Positives = 168/293 (57%), Gaps = 15/293 (5%)

Query: 1   MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMN 60
           ++++L QL+ GLI G+ YALL+LG  +++G++++INFAHG  YM+GAF+ +  +N   ++
Sbjct: 9   LSVLLGQLLLGLINGAFYALLSLGLAIIFGLLRIINFAHGAQYMLGAFVAFLGLNYLGVS 68

Query: 61  FFVALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRA 120
           ++ AL++A L    LG+ IE    R +     +  L+   G++ ++E   V L G +  +
Sbjct: 69  YWFALVLAPLVVGCLGMAIERGLLRRIAGEDHLYGLLLTFGLALIVEGSFVKLFGVSGSS 128

Query: 121 FPQ-AIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQ 179
           +P   +    ++LG + L   +  ++  +L++ +    ++++T++G  +RA + +    Q
Sbjct: 129 YPMPELLRGGFNLGFMFLPTYRAWVIVAALVVCLATWYVIERTRLGSYLRAGTENPKLMQ 188

Query: 180 LMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKS------FVAAVLG 233
             GINV   ++ T+  G ALA  AGVL A       P+  VTPG+ S      F   V+G
Sbjct: 189 GFGINVPLLVTLTYGYGVALAAFAGVLAA-------PIYAVTPGMGSNLLIVVFAVVVIG 241

Query: 234 GIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILGK 286
           G+G I GA + G  +GL+E     F   +  + +V+ +++ +L++RPAG+ GK
Sbjct: 242 GMGSILGAIVTGIAMGLIEGLTKVF-YPEAANTVVFLVMVAVLLIRPAGLFGK 293


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: 260
Number of extensions: 22
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: 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