GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5405 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for D-Alanine, ATPase component (characterized)
to candidate 8502075 DvMF_2788 ABC transporter related (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5405
         (254 letters)



>FitnessBrowser__Miya:8502075
          Length = 243

 Score =  314 bits (805), Expect = 9e-91
 Identities = 154/241 (63%), Positives = 190/241 (78%), Gaps = 1/241 (0%)

Query: 14  IIQMQGVNKWYGQ-FHVLKDINLNVKQGERIVLCGPSGSGKSTTIRCLNRLEEHQQGRIV 72
           +I+   V+KWY    HVL+DI L +KQGE +V+CGPSGSGKST IRC+N+LE  Q+G IV
Sbjct: 1   MIKFDHVHKWYASGLHVLQDITLEIKQGEVVVICGPSGSGKSTLIRCINKLEPIQKGHIV 60

Query: 73  VDGVELTNDLKQIEAIRREVGMVFQHFNLFPHLTILQNCTLAPMWVRKMPKRKAEEIAMH 132
           VDGV++ +    +  +R EVG VFQ FNL+PH+T+L+N TLAP+ VR  P+ +AE+ AM 
Sbjct: 61  VDGVDINDPRTNLTMLRAEVGFVFQQFNLYPHMTVLENITLAPLLVRNTPRAEAEKTAME 120

Query: 133 YLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMKPKIMLFDEPTSALDPEMVKEVLDTM 192
            LE+V IP++A  YPGQLSGGQQQRVAIAR L MKP+IMLFDEPTSALDPEM+ EVLD M
Sbjct: 121 LLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVM 180

Query: 193 IGLAEDGMTMLCVTHEMGFARTVANRVIFMDKGEIVEQAAPNDFFDNPQNDRTKLFLSQI 252
             LA +GMTM+CVTHEMGFAR VA+RVIFMD+G +VE+  P  FF NP +DRTK FLS+I
Sbjct: 181 RQLAREGMTMVCVTHEMGFAREVADRVIFMDQGVMVEENTPEAFFSNPVHDRTKEFLSKI 240

Query: 253 L 253
           L
Sbjct: 241 L 241


Lambda     K      H
   0.322    0.137    0.407 

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: 211
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: 254
Length of database: 243
Length adjustment: 24
Effective length of query: 230
Effective length of database: 219
Effective search space:    50370
Effective search space used:    50370
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 (21.9 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