GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Pseudomonas fluorescens FW300-N2E2

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_3577 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3577 Branched-chain amino
           acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
          Length = 290

 Score =  272 bits (696), Expect = 6e-78
 Identities = 141/290 (48%), Positives = 200/290 (68%), Gaps = 27/290 (9%)

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

Query: 72  TFNQKSGKQYLLERLPD-FRIT-----------------------KEARVARTFQNIRLF 107
             N +  +  +++ L + FR T                         A +ARTFQNIRLF
Sbjct: 63  ELNVRGEQTNVIKLLGEAFRPTDFVSPKSFASRLYYKMFGGTHLVNRAGLARTFQNIRLF 122

Query: 108 SGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADD 167
             ++VLENLLVAQH   M  +   + G++    Y++  ++A++ A +WLE  DL+D A+ 
Sbjct: 123 KEMSVLENLLVAQH---MWVNRSMVAGILNTKGYRKAESDALDHAFYWLEVVDLVDCANR 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+ ++NDP+VIAAYLG ++EE+
Sbjct: 240 IEHDMGMVMSISDHIVVLDHGNVIAEGGPEAIRNDPKVIAAYLGADEEEL 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: 250
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 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, 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