Aligments for a candidate for xylG in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for xylG 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)



>lcl|FitnessBrowser__Phaeo:GFF2274 PGA1_c23060 ribose import
           ATP-binding protein RbsA
          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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources