GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylG 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)



>lcl|FitnessBrowser__Miya:8502321 DvMF_3029 ABC transporter related
           (RefSeq)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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