GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>FitnessBrowser__psRCH2:GFF4209
          Length = 383

 Score =  226 bits (576), Expect = 8e-64
 Identities = 132/334 (39%), Positives = 200/334 (59%), Gaps = 20/334 (5%)

Query: 4   LKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELD 63
           LKI  + K F+    +  + L ++  E    +G SG GKSTLLR++AG E  + G I LD
Sbjct: 23  LKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLD 82

Query: 64  GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILEL 123
           G+DIT++ P +R + M+FQ+YAL+PHM+V +N++F L   G+ KAE+E++V E   ++++
Sbjct: 83  GQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLVQM 142

Query: 124 GPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKEL 183
               +RKP QLSGGQRQRVA+ R++ + PK+ L DEP+  LD  LR QM+LEL+++ + +
Sbjct: 143 TQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIERV 202

Query: 184 QATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM--GF 241
             T + VTHDQ EAMTMA+++ +++ G I QVGSP+D+Y  PA+  V  F+G   +  G 
Sbjct: 203 GVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIGNVNLFDGE 262

Query: 242 L---KGKITRVDSQGCEVQLDAGTRVSLPLGGRHLSVGSAVTLGIRPEHL-------ELA 291
           L    G    + S G E  +  G  +S     +       +T  IRPE L       EL 
Sbjct: 263 LIEDMGDHAVIASPGLENPIYVGHGISTRAEDKQ------ITYAIRPEKLLIGTELPELE 316

Query: 292 KPG-DCALQVTADVSERLGSDTFCHVRTASGEAL 324
           +PG + A  V  D++  LG  +  +++  SG  L
Sbjct: 317 RPGYNWAKGVVHDIA-YLGGHSVYYIKLPSGGVL 349


Lambda     K      H
   0.320    0.137    0.389 

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: 324
Number of extensions: 12
Number of successful extensions: 1
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: 367
Length of database: 383
Length adjustment: 30
Effective length of query: 337
Effective length of database: 353
Effective search space:   118961
Effective search space used:   118961
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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