GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Desulfovibrio vulgaris Miyazaki F

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= BRENDA::Q70HW1
         (384 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  233 bits (595), Expect = 5e-66
 Identities = 122/258 (47%), Positives = 172/258 (66%), Gaps = 10/258 (3%)

Query: 1   MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60
           M+ V L ++ K + G T   V   NL+I   E    +GPSGCGKTTTLRM+AG ED+ +G
Sbjct: 1   MSYVRLVNVTKRFGGVT--AVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDG 58

Query: 61  NLYIGDRRVND------VPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDR 114
            +++GDR ++       +PP+ RD  MVFQ +A++PH++VY+N+AF L++R++  AEIDR
Sbjct: 59  EIHVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDR 118

Query: 115 RVQEAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQM 174
           R +EA     +A +  + P  LSGG +QRVAL RA+   P V L+DEPLS+LD  LR +M
Sbjct: 119 RTREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEM 178

Query: 175 RAEIRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAG 234
           R EI+ L +    +++YVTHDQ+EAM + DRI+VMR+GV+QQ  TP  VY+ P N FV G
Sbjct: 179 RFEIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFG 238

Query: 235 FIGSPAMNFIRGEIVQDG 252
           FIG    NF+   +  +G
Sbjct: 239 FIG--LSNFLDVNLTPEG 254


Lambda     K      H
   0.321    0.138    0.395 

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: 368
Number of extensions: 12
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: 384
Length of database: 354
Length adjustment: 30
Effective length of query: 354
Effective length of database: 324
Effective search space:   114696
Effective search space used:   114696
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: 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