Alignments for a candidate for xylG in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Collimonas pratensis Ter91

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_099047275.1 CPter91_RS07335 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_001584185.1:WP_099047275.1
          Length = 510

 Score =  407 bits (1046), Expect = e-118
 Identities = 221/491 (45%), Positives = 326/491 (66%), Gaps = 6/491 (1%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           + +++I KRFPGV AL     +   GEVHA++GENGAGKSTLMK++AGVY  D GEI   
Sbjct: 1   MSLENITKRFPGVLALDNCRFDLQRGEVHALMGENGAGKSTLMKVLAGVYPKDSGEIRIA 60

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKR--GIFIDYKKMYREAE 122
           G+ V    P  A   GI  + QEL++M++L+ A+NIF+G E +   G+F+D   + R+  
Sbjct: 61  GQLVEIPTPRAAQALGIGIIHQELNLMNHLTAAQNIFIGREPRGRLGMFLDEDALNRKTR 120

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           +   E   +++DP   + + ++A QQMVEIA+A+   ++VLI+DEPT++L   E E LF 
Sbjct: 121 EIF-ERMRLDLDPATLVSELTVAKQQMVEIAKALSFDSRVLIMDEPTAALNNAEIEDLFR 179

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +++ L+  GV I++ISH+++E+ +I ++V+V+RDG+YI T      + E I+ MMVGR++
Sbjct: 180 IIRQLQSHGVGIVYISHKMDELRQISNRVTVMRDGQYIATVPTATTSMETIIGMMVGRQI 239

Query: 243 EKFYIKEAHEPG-EVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG 300
           +          G E+VLEVK L  G   ++V+F+LR+GEILGFAGL+GAGRTE+   +FG
Sbjct: 240 DNSGPDVPDTSGNEIVLEVKGLQRGAFIKDVNFTLRKGEILGFAGLMGAGRTEVARAVFG 299

Query: 301 FRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR-I 359
                 GEI + G RV I  P DA+  GIG + EDRK  GL   + +  NV++ S+++ +
Sbjct: 300 ADRVDAGEILVHGARVSIRSPKDAVAHGIGYLSEDRKHFGLATGLDVKTNVAMSSMNQFL 359

Query: 360 KKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILD 419
            +G F+     ++ A   ++   I+    D+ V  LSGGNQQK+V+AKWL     IL  D
Sbjct: 360 TQGLFLDQAAIRDTAQGYVRQLSIKTPSVDQPVRLLSGGNQQKIVIAKWLLRDCDILFFD 419

Query: 420 EPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAK 479
           EPTRGID+GAK+EIY++++ LA++G  ++MISSELPEVL+MS RI VM  G++ G + A 
Sbjct: 420 EPTRGIDIGAKSEIYKLLNSLAEQGKAIVMISSELPEVLRMSHRILVMCEGRITGELSAA 479

Query: 480 EASQEKVMKLA 490
           EASQEK+M+LA
Sbjct: 480 EASQEKIMQLA 490



 Score =  107 bits (267), Expect = 1e-27
 Identities = 71/226 (31%), Positives = 117/226 (51%), Gaps = 8/226 (3%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           +N  F L+RGE+    G  GAG++ LM+ + G  PK  GEI I G+ VEI  P  A   G
Sbjct: 17  DNCRFDLQRGEVHALMGENGAGKSTLMKVLAGVYPKDSGEIRIAGQLVEIPTPRAAQALG 76

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFK--REKELADWAIKTFDIRPA 386
           IG++ ++   L L+  ++   N+ +    R + G F+       K    +     D+ PA
Sbjct: 77  IGIIHQE---LNLMNHLTAAQNIFIGREPRGRLGMFLDEDALNRKTREIFERMRLDLDPA 133

Query: 387 YPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVG 446
                V  L+   QQ V +AK L+   ++LI+DEPT  ++     +++RI+ QL   GVG
Sbjct: 134 ---TLVSELTVAKQQMVEIAKALSFDSRVLIMDEPTAALNNAEIEDLFRIIRQLQSHGVG 190

Query: 447 VIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           ++ IS ++ E+ Q+S+R+ VM  G+    +     S E ++ +  G
Sbjct: 191 IVYISHKMDELRQISNRVTVMRDGQYIATVPTATTSMETIIGMMVG 236



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 59/244 (24%), Positives = 118/244 (48%), Gaps = 10/244 (4%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +LEVK + +       +K V+     GE+    G  GAG++ + + + G  + D GEI+ 
Sbjct: 255 VLEVKGLQRGA----FIKDVNFTLRKGEILGFAGLMGAGRTEVARAVFGADRVDAGEILV 310

Query: 64  EGRGVRWNHPSEAINAGIVTVFQE---LSVMDNLSVAENIFMGDEEK---RGIFIDYKKM 117
            G  V    P +A+  GI  + ++     +   L V  N+ M    +   +G+F+D   +
Sbjct: 311 HGARVSIRSPKDAVAHGIGYLSEDRKHFGLATGLDVKTNVAMSSMNQFLTQGLFLDQAAI 370

Query: 118 YREAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKET 177
              A+ ++++        ++ +   S   QQ + IA+ + +   +L  DEPT  +     
Sbjct: 371 RDTAQGYVRQLSIKTPSVDQPVRLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDIGAK 430

Query: 178 EKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMM 237
            ++++++ SL E+G AI+ IS  L E+  +  ++ V+ +G   G  S    ++EKI+++ 
Sbjct: 431 SEIYKLLNSLAEQGKAIVMISSELPEVLRMSHRILVMCEGRITGELSAAEASQEKIMQLA 490

Query: 238 VGRK 241
             R+
Sbjct: 491 TLRE 494


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: 643
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 494
Length of database: 510
Length adjustment: 34
Effective length of query: 460
Effective length of database: 476
Effective search space:   218960
Effective search space used:   218960
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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