GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Klebsiella michiganensis M5al

Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate BWI76_RS26290 BWI76_RS26290 glycerol-3-phosphate ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF4321
         (386 letters)



>FitnessBrowser__Koxy:BWI76_RS26290
          Length = 356

 Score =  313 bits (803), Expect = 4e-90
 Identities = 170/364 (46%), Positives = 234/364 (64%), Gaps = 9/364 (2%)

Query: 1   MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60
           MA L+L+ V K++  G    ++ + L + +GEF+++VGPSGCGKSTL+  +AGLE +T G
Sbjct: 1   MAGLKLQAVTKSWD-GKTQVIQPLTLDVADGEFIVMVGPSGCGKSTLLRMVAGLERVTSG 59

Query: 61  AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120
            I I  + V+ M PKDR IAMVFQ+YALYP MSV EN+ +GLKIR + +  I   V   A
Sbjct: 60  DIWIDRKRVTEMEPKDRGIAMVFQNYALYPHMSVEENMAWGLKIRGLGKGLIAERVQEAA 119

Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           ++L+++ LL R+P +LSGGQ+QRVAMGRA+ R P ++LFDEPLSNLDAKLRV+MR E++ 
Sbjct: 120 RILELDGLLKRRPRELSGGQRQRVAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRLELQH 179

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240
           +H+RLKTT++YVTHDQ+EAMTL  +V VM  G+ +Q GTP E+Y  PA++FVASFIGSP 
Sbjct: 180 LHRRLKTTSLYVTHDQVEAMTLAQRVMVMNKGVAEQIGTPVEVYEKPASRFVASFIGSPA 239

Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300
           MN +  R+     R    L  G     L +N+       R + LG+RPE   L++    +
Sbjct: 240 MNLLEGRVSDDGSRFE--LAGGML---LPINSEHRRYAGRKMTLGIRPEHFALSS---QA 291

Query: 301 ASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAN 360
              +   +   E  G D L   +  + K+  RL     PQ G TL L      + LFD+ 
Sbjct: 292 EGGVPLVMDTLEILGADNLAHGRWGEQKLVVRLPHQQRPQAGSTLWLHLPQESLHLFDSE 351

Query: 361 TGER 364
           TG+R
Sbjct: 352 TGQR 355


Lambda     K      H
   0.318    0.135    0.382 

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: 359
Number of extensions: 14
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: 386
Length of database: 356
Length adjustment: 30
Effective length of query: 356
Effective length of database: 326
Effective search space:   116056
Effective search space used:   116056
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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