GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Dechlorosoma suillum PS

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  204 bits (519), Expect = 3e-57
 Identities = 113/297 (38%), Positives = 178/297 (59%), Gaps = 16/297 (5%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           G+ VA++++SL I  GE + L+GPSGCGK+T LR++AG+ET  EG++  E      + A+
Sbjct: 13  GNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHAR 72

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLP---DDEIRQRVEETTDMLGISDLLDR 135
           +R +  VFQ YAL+ H +V  N++FGL          + EIR+RV +   ++ +  L DR
Sbjct: 73  ERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADR 132

Query: 136 KPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVY 195
            P QLSGGQ+QR+AL RA+  +P+V L+DEP   LD K+R E+R  L+RL  E+ +++V+
Sbjct: 133 YPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVF 192

Query: 196 VTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255
           VTHDQ EA+ + DRV V++ G ++QVG+P + Y  P + FV  F+G  ++N+F   + G 
Sbjct: 193 VTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLG--NVNVFHSRVHG- 249

Query: 256 TFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQG 312
                      +   RD +         IRP D+ + +  +   + +A+V  V+  G
Sbjct: 250 ---------AWAEVARDDVPAGQEAVAFIRPHDIDI-DTVATPESLEAKVSYVQTIG 296


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: 348
Number of extensions: 15
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: 360
Length adjustment: 30
Effective length of query: 353
Effective length of database: 330
Effective search space:   116490
Effective search space used:   116490
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: 49 (23.5 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