GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mtlK in Pseudomonas simiae WCS417

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase

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



>lcl|FitnessBrowser__WCS417:GFF4321 PS417_22130 sugar ABC
           transporter ATPase
          Length = 386

 Score =  305 bits (782), Expect = 1e-87
 Identities = 166/362 (45%), Positives = 241/362 (66%), Gaps = 9/362 (2%)

Query: 1   MANLKIKNLQKGFEGF--SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGG 58
           MA L+++N+ K +       +K I+L + + EF++ VGPSGCGKSTL+  IAGLE ++GG
Sbjct: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60

Query: 59  TIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAA 118
            I +  +D++ +SP  RD+AMVFQ+YALYP MSVR+N+ F L +  + +A+++ +V+  A
Sbjct: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120

Query: 119 RILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLR 178
           ++L++  +L RKP QLSGGQ+QRVA+GRA+ R PKI+LFDEPLSNLDA LRV+MR E+  
Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180

Query: 179 LHKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPK 238
           +H+ L+ T +YVTHDQ+EAMT+ DKV V+  G I+Q G+P ++Y+ PAN FVA F+G+P 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240

Query: 239 MGFLKGKITRVDSQGCEVQLDAG-TRVSLPLGGRHLSVGSA-VTLGIRPEHLELAK-PGD 295
           M F+  ++ R D +     LD+G  R  L L      +    V LG+RPE + LA   GD
Sbjct: 241 MNFVPLRLQRKDGR-LVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGD 299

Query: 296 CALQVTAD--VSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHCHLFD 353
            A  + A+  V+E  G DT   V+  +   +  R+  D+A + GETL+L  D     LFD
Sbjct: 300 SASSIRAEVQVTEPTGPDTLVFVQ-LNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358

Query: 354 AD 355
           A+
Sbjct: 359 AN 360


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: 385
Number of extensions: 17
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: 367
Length of database: 386
Length adjustment: 30
Effective length of query: 337
Effective length of database: 356
Effective search space:   119972
Effective search space used:   119972
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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