GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Desulfovibrio vulgaris Miyazaki F

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)

Query= TCDB::Q52666
         (263 letters)



>FitnessBrowser__Miya:8502075
          Length = 243

 Score =  320 bits (820), Expect = 2e-92
 Identities = 157/242 (64%), Positives = 191/242 (78%), Gaps = 1/242 (0%)

Query: 23  IQISQMNKWYGQ-FHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIV 81
           I+   ++KWY    HVL+DI L + +GE +VI GPSGSGKST+IRCIN+LE  Q G I+V
Sbjct: 2   IKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIVV 61

Query: 82  DGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYY 141
           DG+++     N+  +R+EVG VFQ FNL+PH+T+LEN+TLAP+ VR  P+ EAE+TAM  
Sbjct: 62  DGVDINDPRTNLTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKTAMEL 121

Query: 142 LEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMI 201
           LEKV IP++A  YPGQLSGGQQQRVAIAR L MKP+IMLFDEPTSALDPEMI EVLD M 
Sbjct: 122 LEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVMR 181

Query: 202 QLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQFLSQIL 261
           QLA EGMTM+CVTHEMGFA+ VA+RVIFM  G +VE+N P  FF NP  +RTK+FLS+IL
Sbjct: 182 QLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFLSKIL 241

Query: 262 GH 263
            H
Sbjct: 242 TH 243


Lambda     K      H
   0.320    0.134    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: 233
Number of extensions: 5
Number of successful extensions: 1
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: 263
Length of database: 243
Length adjustment: 24
Effective length of query: 239
Effective length of database: 219
Effective search space:    52341
Effective search space used:    52341
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: 46 (22.3 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