GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araV in Desulfacinum infernum DSM 9756

Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_073038605.1 BUB04_RS08650 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= TCDB::Q97UF2
         (371 letters)



>NCBI__GCF_900129305.1:WP_073038605.1
          Length = 368

 Score =  199 bits (506), Expect = 1e-55
 Identities = 115/298 (38%), Positives = 178/298 (59%), Gaps = 20/298 (6%)

Query: 1   MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60
           M  I+++ ++K FKK       V + ++T+       ++GPSG GK+T LR+IAGLEE T
Sbjct: 1   MAEIKLDQVNKRFKKNWV----VRDFTLTVADKEFVVLVGPSGCGKSTTLRMIAGLEEVT 56

Query: 61  SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120
           SG I      V+      + P+ R IAMVFQ++ALYP+M V+ N+AF L    VP+D+I+
Sbjct: 57  SGEISIGGRVVNH-----VPPKDRDIAMVFQSYALYPHMNVYKNMAFGLMNRGVPRDEID 111

Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180
            +VK+ +E LG+S +L R P +LSGGQ QR A+ RA+V+DP+  L DEP SNLDA++R  
Sbjct: 112 RRVKQAAEILGISDLLQRRPAQLSGGQRQRVAMGRAIVRDPQAFLFDEPLSNLDAKLRVQ 171

Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240
            RA + K+    + T + V+HD  +   +A++  V+ +GK  Q+G P E+YE PA   +A
Sbjct: 172 MRAELAKLHERLQSTIVYVTHDQIEAMTLADRIVVMKDGKIMQVGPPLEVYERPANRFVA 231

Query: 241 RLTG--EINLIQAKIIENNAII------ANLKVPLNNM-ELKGQSN--IVIGLRPDDL 287
              G   +N +  +++E    +        LKVP +     +G  N  ++ G+RP+D+
Sbjct: 232 GFIGSPSMNFLDVRLVEEAGDLWVDGESFRLKVPRHRAPAFRGHVNRPVIFGIRPEDV 289


Lambda     K      H
   0.317    0.136    0.374 

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: 305
Number of extensions: 16
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: 371
Length of database: 368
Length adjustment: 30
Effective length of query: 341
Effective length of database: 338
Effective search space:   115258
Effective search space used:   115258
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 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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