GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas fluorescens FW300-N1B4

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf1N1B4_1380 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)

Query= uniprot:Q1MCU1
         (463 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1380
          Length = 427

 Score =  317 bits (812), Expect = 5e-91
 Identities = 196/427 (45%), Positives = 251/427 (58%), Gaps = 29/427 (6%)

Query: 16  VRKGLTEALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAAIGRFAMVV 75
           +++ L +A+ A +++  +F   VG+  D    N       W      VA+   GRFA+ +
Sbjct: 11  LKRSLVDAILAGLVALIVFGPIVGVVLDGYGFNLEATRVAW-----IVAIVMAGRFALSL 65

Query: 76  FIRPNIDRRKLSKAREGELDISTEKSFFHRHFLKIALIALLLYPMVVVAIKGPQGSLTYV 135
           F++     R L         +      +      I  +      M+V+A+  P  S +Y+
Sbjct: 66  FLQTPKGLRILEGFESTGSGVHVLPPDYKSRLRWIIPV------MIVIAVVFPFFSNSYL 119

Query: 136 DNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLS 195
               I  LIYV+L  GLNIVVGLAGLLDLGYVAFYA+GAY  AL   Y GL FW +LPL+
Sbjct: 120 LGVVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLA 179

Query: 196 GIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF 255
            I A L G ILGFPVLRL GDYLAIVTL FGEIIRL+L NW  +T G  G+++ P  T F
Sbjct: 180 AITAGLAGCILGFPVLRLHGDYLAIVTLGFGEIIRLILNNWLSLTGGPNGMAA-PLPTFF 238

Query: 256 GIPFDATAGGFAKLFHLPISSAY---YKIFLFYLILALCMLTA-YVTIRLRRMPIGRAWE 311
           G+ F   A      FH     AY    K +  Y +L L +L   Y+  RL RMP+GRAWE
Sbjct: 239 GLEFGKRAKEGGVPFHEFFGIAYNPDVKYYFIYAVLFLVVLAVLYIKHRLTRMPVGRAWE 298

Query: 312 ALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILA 371
           ALREDEIACRS+G+N V  KL+AF  GA  AG AG FFA  QGFV+P SF F ESA+ILA
Sbjct: 299 ALREDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFATYQGFVNPTSFTFFESALILA 358

Query: 372 IVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVML 431
           IVVLGGMGS  G+ IAA V+    ELLR  +              YR+L+FG+ MV++M+
Sbjct: 359 IVVLGGMGSTIGVVIAAFVLTVAPELLRGFA-------------EYRVLLFGILMVLMMI 405

Query: 432 FKPRGFV 438
           ++PRG +
Sbjct: 406 WRPRGLI 412


Lambda     K      H
   0.330    0.145    0.432 

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: 676
Number of extensions: 43
Number of successful extensions: 5
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: 463
Length of database: 427
Length adjustment: 32
Effective length of query: 431
Effective length of database: 395
Effective search space:   170245
Effective search space used:   170245
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: 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:

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