GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Desulfovibrio vulgaris Miyazaki F

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= reanno::Phaeo:GFF2754
         (331 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  221 bits (564), Expect = 2e-62
 Identities = 125/304 (41%), Positives = 176/304 (57%), Gaps = 16/304 (5%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M+ ++L NV K FG V  +  +NL +  GE    +GPSGCGK+T LR+++G ED   GEI
Sbjct: 1   MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI 60

Query: 61  SIGGQTVTTT------PPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARV 114
            +G + ++        PP KR   MVFQ++A++PHLSV EN+A  L+  R    EI  R 
Sbjct: 61  HVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRT 120

Query: 115 AEASRMLSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRL 174
            EA    SL D   + P +LSGG +QRVA+ RA+   P + L DEPLS+LD  LR   R 
Sbjct: 121 REALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRF 180

Query: 175 EIARLHRQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFI 234
           EI  L R    S++YVTHDQ EAM L+D+I+V+R+G ++QVGTP+++Y NPAN FV  FI
Sbjct: 181 EIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFI 240

Query: 235 GAPAMNFVPAQRLGGNPGQFIGIRPEYARISPVGPLAGEVIHVEKLGGDTNILVDMGEDL 294
           G    NF+        P   + +    AR++P  P +  ++   +       L     ++
Sbjct: 241 G--LSNFLDVNL---TPEGLVRVNGGDARVTPATPPSARLVSAGRAA-----LASRPSEI 290

Query: 295 TFTA 298
            FTA
Sbjct: 291 DFTA 294


Lambda     K      H
   0.320    0.137    0.391 

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: 319
Number of extensions: 9
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: 331
Length of database: 354
Length adjustment: 29
Effective length of query: 302
Effective length of database: 325
Effective search space:    98150
Effective search space used:    98150
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.

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