GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Herbaspirillum seropedicae SmR1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS22750 HSERO_RS22750 sugar ABC transporter ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__HerbieS:HSERO_RS22750
          Length = 377

 Score =  289 bits (739), Expect = 1e-82
 Identities = 171/376 (45%), Positives = 225/376 (59%), Gaps = 20/376 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA + +  + K Y  +G  D++A   ++LDI DGEF VLVGPSGCGKST LRM+ GLE +
Sbjct: 1   MAHVNIKQLRKTY--DGRADVLA--GLNLDIRDGEFCVLVGPSGCGKSTLLRMLCGLEEI 56

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           + GEL +  +V+N +   +R IAMVFQSYALYPH +V  NM+FGL+ + G    +I  R+
Sbjct: 57  SGGELAIGGQVVNHLPPAERGIAMVFQSYALYPHMNVYKNMAFGLKVA-GNSKSDIDARI 115

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
                +L I  LL R P +LSGGQ+QRVA+GRAIVR P +FL DEPLSNLDA LR + R 
Sbjct: 116 RHAAAILKIDHLLQRLPRELSGGQRQRVAIGRAIVRQPRLFLFDEPLSNLDAALRVQTRL 175

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+ +L  +L  T VYVTHDQ EAMT+GD++ V+ +G +QQ GTPL+ Y +P NLFVAGFI
Sbjct: 176 EIAKLHRQLAATIVYVTHDQVEAMTLGDKIVVMHEGRIQQAGTPLELYQQPQNLFVAGFI 235

Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATR-----DQLGGASG--LTLGIRPEDVTVGE 293
           G P MN F G ++       G    ++G  R     D LG   G  +TLG+R E +  G 
Sbjct: 236 GSPKMNFFQGVVT--RCDDSGVQVEIAGGLRLLADVDPLGVTPGAAVTLGLRAEQIREG- 292

Query: 294 RRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPED 353
                +     V +VE  G  N +   +V  D G        G   V+ G    +S    
Sbjct: 293 -LGDGQPLHGVVNLVEHLGEANFL---YVTLDGGHDIVVRGDGNRNVDIGQPIALSVHSH 348

Query: 354 AIHLFDGETGDALKNR 369
           A HLFD + G AL+ R
Sbjct: 349 AFHLFDAQ-GQALRRR 363


Lambda     K      H
   0.316    0.136    0.384 

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: 476
Number of extensions: 22
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: 383
Length of database: 377
Length adjustment: 30
Effective length of query: 353
Effective length of database: 347
Effective search space:   122491
Effective search space used:   122491
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: 42 (22.0 bits)
S2: 50 (23.9 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