GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Desulfovibrio vulgaris Miyazaki F

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  284 bits (726), Expect = 6e-81
 Identities = 156/490 (31%), Positives = 284/490 (57%), Gaps = 5/490 (1%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           + P++ +  I K F  V A   ++++  PG + A++GENGAGKSTLM I+AG  + D G 
Sbjct: 26  LPPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGT 85

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           I+ +G    +  P +A+ AGI  V+Q   ++D+++VAEN+ +G  +   + +   +M R+
Sbjct: 86  IVVDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLG--QSPDMLLRPARM-RD 142

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
               + E +G+ +DP  ++G  S+  +Q VEI + +Y+ ++VLILDEPT+ LT +ET++L
Sbjct: 143 EVAALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQL 202

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIV-EMMVG 239
           FE +  + ++G A++FISH+L+E+  + D++++LR GE +   S  ++  + ++   MVG
Sbjct: 203 FEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVG 262

Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           R +      +   P + VL V++LSG    +VS  +RRGEI+  AG+ G G+ EL+E I 
Sbjct: 263 RDVVLQVDAKRLTPVDTVLSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEAIC 322

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359
           G      GE+ I G+            +G+  +PEDR+ L     + ++ N  L + ++ 
Sbjct: 323 GLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQF 382

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
            KG F+            +  ++++P         LSGGN QK+V+ +    KP++++ +
Sbjct: 383 AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAE 442

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
            PT+G+D+ A  E++  + + A+   GV++++ +L E L+++DRIAVM  G+   + D  
Sbjct: 443 NPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDVFDKD 501

Query: 480 EASQEKVMKL 489
           + ++ + + L
Sbjct: 502 DTAKVQAIGL 511


Lambda     K      H
   0.318    0.138    0.385 

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: 593
Number of extensions: 34
Number of successful extensions: 9
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: 494
Length of database: 537
Length adjustment: 35
Effective length of query: 459
Effective length of database: 502
Effective search space:   230418
Effective search space used:   230418
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 (21.7 bits)
S2: 52 (24.6 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