GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Phaeobacter inhibens BS107

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 GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  463 bits (1191), Expect = e-135
 Identities = 244/494 (49%), Positives = 342/494 (69%), Gaps = 3/494 (0%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+L ++ I K FPGV AL GVS+   PGEVHA++GENGAGKSTLMK++ G++QPDEG+II
Sbjct: 6   PVLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQII 65

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGD-EEKRGIFIDYKKMYREA 121
              + V  + P +A   GIV + QELS+ D LSVAENI++G+   KR   +D+ ++  + 
Sbjct: 66  VAEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKT 125

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
              + E+  +  + + ++G  SIA QQMVEIARA+   AK +I DEPT+SLT  E   LF
Sbjct: 126 NAIL-EKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLF 184

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
           EV+  L+E+GV I +ISHR+EEIF+I D++SVLRDG+Y GT +     +E + +MM+GRK
Sbjct: 185 EVISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRK 244

Query: 242 LEKFYIKEAHEPGEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           L+    +  HE GEV LEV+ LS G  FE+V+F +RRGE++GF GLVGAGRTE+ ET+FG
Sbjct: 245 LDLSRNEAHHELGEVALEVRGLSCGSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFG 304

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIK 360
            R    G I+++G  V I  P DAIE+GI LVPEDRK  GL+L M+   N++LP +D +K
Sbjct: 305 LRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLK 364

Query: 361 KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
            GPF++   E  + D      DIR     + V  LSGGNQQK+V+ KWL+++P +LI+DE
Sbjct: 365 AGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDE 424

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PTRGIDVG+KAEI+ ++  LA +G  VI+ISSE+PEVL ++DRI  M  G++     ++E
Sbjct: 425 PTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEE 484

Query: 481 ASQEKVMKLAAGLE 494
            ++E ++   +GL+
Sbjct: 485 VTEENLIAAISGLD 498



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 58/236 (24%), Positives = 112/236 (47%), Gaps = 23/236 (9%)

Query: 23  VSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIV 82
           V+ E   GEV    G  GAG++ + + + G+  P  G I  +G  V    P +AI  GI 
Sbjct: 275 VNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERGIS 334

Query: 83  TVFQE---------LSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFMKEEFGIEI 133
            V ++         ++  DN+++ +     D+ K G F+        AE  + +++  ++
Sbjct: 335 LVPEDRKGQGLVLGMNCRDNMTLPQV----DDLKAGPFVA-----DGAEIAIFDQYRDKL 385

Query: 134 DP-----EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLK 188
           D      ++ +G  S   QQ + I + +  +  VLI+DEPT  +      ++  +++ L 
Sbjct: 386 DIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLA 445

Query: 189 EKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLEK 244
            +G A+I IS  + E+  + D++  +  G  + T + E +T+E ++  + G   EK
Sbjct: 446 AQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLDTEK 501


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: 697
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 503
Length adjustment: 34
Effective length of query: 460
Effective length of database: 469
Effective search space:   215740
Effective search space used:   215740
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