GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Pseudomonas fluorescens FW300-N1B4

Align Amino-acid permease GAP1 (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease

Query= SwissProt::Q5AG77
         (582 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139 Gamma-aminobutyrate
           permease
          Length = 501

 Score =  226 bits (577), Expect = 1e-63
 Identities = 146/434 (33%), Positives = 229/434 (52%), Gaps = 23/434 (5%)

Query: 43  DKLT----GVDDIPDRELTDIERININAANSNLQRKLKTRHLQMIAIGSSIGTGLFVGTG 98
           D+LT     +  I   +   +  +N   +N  L +  K RH+ M++I   IG GLFVG+G
Sbjct: 14  DRLTLSQYALTSITREQKKTMNNLNSRDSNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSG 73

Query: 99  GALSTGGPAAIVLAWAISAISVFMTMQGLGELAVAFPVSGGFNLYASKFLEPGIGFAVGW 158
            A++  GPA ++LA+  S + V + M+ LGE+AVA P +G F+ YA + +    GF +GW
Sbjct: 74  HAIAAAGPA-VLLAYLFSGLLVVLVMRMLGEMAVANPDTGSFSTYADQAIGRWAGFTIGW 132

Query: 159 NYFLQFFVLLPLELVAGAITIKYWNASINSDVFVIIFWFVVLVITMLGVRWYGEAELVFC 218
            Y+  + +++P+E +A    +  W   I++ +F +    +++V  +  V  YGE E  F 
Sbjct: 133 LYWWFWVLVIPIEALAAGHVLNQWFPQIDTWLFALTSIILLVVTNLFSVSKYGEFEFWFA 192

Query: 219 TIKVIAVIGFIILGIVLICGGGPNHEFIG-GKYWREPGPFA-NSFKGFASSLITAAFSFG 276
             KV+A+IGFI LG  ++ G  P  E  G  +   E G FA N       + IT  FSF 
Sbjct: 193 MAKVVAIIGFIGLGFAVLMGWIPEREASGLSRLMEEHGGFAPNGLSAVVGAFITIMFSFI 252

Query: 277 GTEMIALTASESSNVRHALPKAIKQVFWRIVIFYLGSIIMIATLVPYNDKRLLGSSSVDV 336
           GTE + + A+ESSN    + KA + V WRI +FYL SI ++ ++VP+ND  L    S   
Sbjct: 253 GTEAVTIAAAESSNPAQNIAKATRSVIWRIGVFYLLSIFVVISVVPWNDPLLASVGS--- 309

Query: 337 TASPFTIAIVNGGIKGLPSVINAVILISVLSVGNASVYATSRTLNSLAEQGMAPKWTGYI 396
               +  A+    I     +++ V+LI+V S  N+S+Y  SR L SL ++G APK     
Sbjct: 310 ----YQRALELMNIPHAKLMVDVVVLIAVASCMNSSIYIASRMLFSLGKRGDAPKPLKVT 365

Query: 397 DRAGRPLFAILITNVFG----LFALIAADNEKQVVAFNWLLALSGLSSIFTWMSINLSHI 452
              G P  A++ + V G    LF+            F +LLA SG  ++  ++ I +S +
Sbjct: 366 SSDGVPRAAVIASTVLGAGVTLFSYFMPAG-----LFQFLLASSGAIALLVYLVIAVSQL 420

Query: 453 RFRRAMKVQNRSLT 466
           R R+ +  QN +LT
Sbjct: 421 RMRKILLRQNVTLT 434


Lambda     K      H
   0.325    0.140    0.430 

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: 657
Number of extensions: 35
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: 582
Length of database: 501
Length adjustment: 35
Effective length of query: 547
Effective length of database: 466
Effective search space:   254902
Effective search space used:   254902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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 paper from 2022 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