Alignments for a candidate for xylG in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Rhodobacter viridis JA737

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 WP_110806491.1 C8J30_RS14105 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_003217355.1:WP_110806491.1
          Length = 513

 Score =  426 bits (1096), Expect = e-124
 Identities = 225/493 (45%), Positives = 332/493 (67%), Gaps = 7/493 (1%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           ILEV  + K FPGV AL  V ++  PG VHA++GENGAGKSTLMKIIAGVY PD GE+ +
Sbjct: 22  ILEVDGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPDRGEVRF 81

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGI-FIDYKKM-YREA 121
            G  +    P +A+N GI  + QEL++M+ ++VAEN+++  E K     ID+ +M    A
Sbjct: 82  AGEKLVIRTPIDALNCGIAMIHQELNLMNTMTVAENVWIRREPKGAFGLIDHARMGTMTA 141

Query: 122 EKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLF 181
           E F      I +DP   +G  ++A +QM+EIA+AV   + VLI+DEPTS++T+ E E LF
Sbjct: 142 ELFAS--LNIHLDPLAIVGDLTVAQKQMIEIAKAVSYNSDVLIMDEPTSAITETEVEHLF 199

Query: 182 EVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRK 241
            +++ L+ +GV I++I+H++ EIFEI D+++V RDG+YI T     +T++ I+ MMVGR+
Sbjct: 200 AIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPASEVTRDDIIRMMVGRE 259

Query: 242 LEKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           + + + K     G+V+L+V+NLS    F+N+SF LR+GEILG AGLVG+GR+ + E +FG
Sbjct: 260 ITEMFPKVDCPIGDVILDVQNLSLPGVFDNISFKLRKGEILGVAGLVGSGRSNVAEALFG 319

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL--DR 358
             P   G+I+I+G+ V +  P  A++ G+  + EDRK+ G  L++  + N+ +  +  D+
Sbjct: 320 VHPAETGDIWIDGEHVVMTSPQVAMDHGLAFLTEDRKETGCFLVLDCLENMQMALITRDK 379

Query: 359 IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418
           +    F+       L         ++      +V  LSGGNQQK+++A+WL   P+ILIL
Sbjct: 380 VNGAGFVQQAEVTRLVQEYSAKLRVKTPNLAERVENLSGGNQQKLLIARWLLTNPRILIL 439

Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478
           DEPTRGIDVGAK+EI+R+++ LA +GV V+MISSELPEVL MSDRI VM  G+++G +D 
Sbjct: 440 DEPTRGIDVGAKSEIHRLITALAGQGVAVLMISSELPEVLGMSDRIMVMHEGRVSGFLDR 499

Query: 479 KEASQEKVMKLAA 491
            EA+Q +VM+LAA
Sbjct: 500 AEATQVRVMELAA 512



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 68/251 (27%), Positives = 122/251 (48%), Gaps = 14/251 (5%)

Query: 251 HEPGEVVLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKR 305
           H  GE +LEV  +  E       +NV   +R G +    G  GAG++ LM+ I G     
Sbjct: 16  HYDGEFILEVDGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPD 75

Query: 306 GGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPF- 364
            GE+   G+++ I  P+DA+  GI ++ ++   L L+  M++  NV +    R  KG F 
Sbjct: 76  RGEVRFAGEKLVIRTPIDALNCGIAMIHQE---LNLMNTMTVAENVWIR---REPKGAFG 129

Query: 365 -ISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTR 423
            I   R   +      + +I    P   V  L+   +Q + +AK ++    +LI+DEPT 
Sbjct: 130 LIDHARMGTMTAELFASLNIH-LDPLAIVGDLTVAQKQMIEIAKAVSYNSDVLIMDEPTS 188

Query: 424 GIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQ 483
            I       ++ I+  L   GVG++ I+ ++ E+ +++D + V   GK    + A E ++
Sbjct: 189 AITETEVEHLFAIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPASEVTR 248

Query: 484 EKVMKLAAGLE 494
           + ++++  G E
Sbjct: 249 DDIIRMMVGRE 259


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: 679
Number of extensions: 31
Number of successful extensions: 8
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: 513
Length adjustment: 34
Effective length of query: 460
Effective length of database: 479
Effective search space:   220340
Effective search space used:   220340
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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