GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Bacteroides thetaiotaomicron VPI-5482

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Btheta:350819
          Length = 463

 Score =  229 bits (583), Expect = 2e-64
 Identities = 118/276 (42%), Positives = 180/276 (65%), Gaps = 11/276 (3%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           GD  A+++++L++  GEF+ ++GPSGCGK+T LR++AG +T +EGE+R+  + +      
Sbjct: 20  GDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRISGKEITQTPPH 79

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRVEETTDMLGISDLLDRKPG 138
            R +  VFQ YAL+PH +V  N++FGL+     P   I ++V+    M+G++D   R   
Sbjct: 80  KRPVNTVFQKYALFPHLNVYDNIAFGLKLKK-TPKQTIGKKVKAALKMVGMTDYEYRDVD 138

Query: 139 QLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVYVTH 198
            LSGGQQQRVA+ RAIV +PEV L+DEPL+ LD K+R +M+ EL+ +   LG+T VYVTH
Sbjct: 139 SLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHKSLGITFVYVTH 198

Query: 199 DQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD--- 255
           DQ EA+T+ D + V+ +G++QQ+GTP+D Y+ P N FVA FIGE   N+ +G++  D   
Sbjct: 199 DQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFIGE--SNILNGTMIHDKLV 256

Query: 256 TFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTV 291
            F G  F+        +  G  + + + IRPED+ +
Sbjct: 257 RFCGTEFE-----CVDEGFGENTPVDVVIRPEDLYI 287


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: 512
Number of extensions: 31
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: 383
Length of database: 463
Length adjustment: 32
Effective length of query: 351
Effective length of database: 431
Effective search space:   151281
Effective search space used:   151281
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.

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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:

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