GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Phaeobacter inhibens BS107

Align SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF2754 PGA1_c27970 ATP-binding transport protein SmoK

Query= TCDB::P54933
         (332 letters)



>lcl|FitnessBrowser__Phaeo:GFF2754 PGA1_c27970 ATP-binding transport
           protein SmoK
          Length = 331

 Score =  346 bits (888), Expect = e-100
 Identities = 180/311 (57%), Positives = 224/311 (72%), Gaps = 1/311 (0%)

Query: 1   MGKITLRNVQKRFGEAVVIPSLDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDVSDGQI 60
           M  + L NV K FG   V+  ++L +EDGEFVVFVGPSGCGKSTLLR+I+GLED + G+I
Sbjct: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60

Query: 61  MIDGRDATEMPPAKRGLAMVFQSYALYPHMTVKKNIAFPLRMAKMEPQEIERRVSNAAKI 120
            I G+  T  PPAKRG+AMVFQSYALYPH++V++N+A  L+  +   +EI  RV+ A+++
Sbjct: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120

Query: 121 LNLTNYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVNMRLEITELH 180
           L+L +YLDRRP +LSGGQRQRVAIGRA+VREP  FLFDEPLSNLDAALR+N RLEI  LH
Sbjct: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180

Query: 181 QSLETTMIYVTHDQVEAMTMADKIVVLNAGRIEQVGSPLTLYRNPANLFVAGFIGSPKMN 240
           + L  +MIYVTHDQ+EAMT+ADKIVVL  GRIEQVG+P+ LY NPAN FVA FIG+P MN
Sbjct: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240

Query: 241 LIEGPEAAKHGATTIGIRPEHIDLSREAGAWEGEVGVSEHLGSDTFLHVHVAGMPTLTVR 300
            +       +    IGIRPE+  +S   G   GEV   E LG DT + V +    T T R
Sbjct: 241 FVPAQRLGGNPGQFIGIRPEYARIS-PVGPLAGEVIHVEKLGGDTNILVDMGEDLTFTAR 299

Query: 301 TGGEFGVHHGD 311
             G+   + G+
Sbjct: 300 LFGQHDTNVGE 310


Lambda     K      H
   0.320    0.137    0.400 

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: 364
Number of extensions: 8
Number of successful extensions: 2
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: 332
Length of database: 331
Length adjustment: 28
Effective length of query: 304
Effective length of database: 303
Effective search space:    92112
Effective search space used:    92112
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: 49 (23.5 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