GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf1N1B4_1379 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1379
          Length = 290

 Score =  266 bits (680), Expect = 4e-76
 Identities = 140/290 (48%), Positives = 196/290 (67%), Gaps = 27/290 (9%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           + +L V+ L M FGG+ A++D S + KR  I ALIGPNGAGKTTVFNC+TGFYK + G I
Sbjct: 3   EVVLSVDKLMMHFGGIKALSDVSLKVKRNSIFALIGPNGAGKTTVFNCLTGFYKASGGHI 62

Query: 72  TFNQKSGKQYLLERLP------DF------------------RITKEARVARTFQNIRLF 107
             N +  K  +++ L       DF                   +   A +ARTFQNIRLF
Sbjct: 63  ELNTRGVKTDVIKMLGEPFKAVDFVSPKSFINRLRYKMFGGTHLINRAGLARTFQNIRLF 122

Query: 108 SGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADD 167
             ++VLENLLVAQH   M  +   + G++    Y++  ++A++ A +WLE  DL+D A+ 
Sbjct: 123 REMSVLENLLVAQH---MWVNRGMLAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANR 179

Query: 168 PAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILL 227
            AG+L YG QRRLEIARAMCT P+++CLDEPAAGLNP+E+  L+A+++ +R E   +++L
Sbjct: 180 LAGELSYGQQRRLEIARAMCTRPQIICLDEPAAGLNPQETEALSAMIRLLRDEHDLTVVL 239

Query: 228 IEHDMSVVMEISDHVVVLEYGQKISDGTPDHVKNDPRVIAAYLGVEDEEV 277
           IEHDM +VM ISDH+VVL++G  I++G P+ +++DP+VIAAYLG E+EEV
Sbjct: 240 IEHDMGMVMSISDHIVVLDHGVVIAEGGPEAIRHDPKVIAAYLGAEEEEV 289


Lambda     K      H
   0.318    0.136    0.386 

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: 241
Number of extensions: 8
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: 290
Length adjustment: 26
Effective length of query: 266
Effective length of database: 264
Effective search space:    70224
Effective search space used:    70224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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