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_082793282.1 CPter91_RS01720 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_001584185.1:WP_082793282.1
          Length = 518

 Score =  449 bits (1156), Expect = e-131
 Identities = 243/495 (49%), Positives = 340/495 (68%), Gaps = 4/495 (0%)

Query: 1   MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60
           ++ IL + ++ KRFPGV AL  VS +   GEVHAI GENGAGKSTLMKII+GVY+ D+G 
Sbjct: 19  LESILSLSNVTKRFPGVLALDRVSFDLKKGEVHAICGENGAGKSTLMKIISGVYRADQGA 78

Query: 61  IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYRE 120
           IIY+G   R+   +EA  AGI  + QEL+++ +LSVAENIF+  E K+G+F+D KKM   
Sbjct: 79  IIYKGSECRFESSTEAQIAGIAIIHQELNLVPHLSVAENIFLAREPKKGLFVDRKKMNAN 138

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A+  + +   + I P + +   SIA QQMVEIA+A+   A+VLI+DEPTSSLT+ ET +L
Sbjct: 139 AQICL-DRLKVNIKPADLVKSLSIAQQQMVEIAKALSLNAEVLIMDEPTSSLTETETGQL 197

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           F ++  LK  GV I++ISHRL+E+  I D+V+V+RDG+++ TD+   +T +KIV  MVGR
Sbjct: 198 FNIINDLKRNGVGIVYISHRLDELRHIVDRVTVMRDGKFVSTDNFSEITIDKIVSKMVGR 257

Query: 241 KLEKFYIKEAHEPGE-VVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETI 298
            LE  + +    P E  +L V+NLS +  F  + F+LR+GEILGFAGL+GAGRTE+   I
Sbjct: 258 ALEDAFPERKSTPTEKTLLTVRNLSRQDDFGPIDFALRQGEILGFAGLIGAGRTEVARAI 317

Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358
           FG  P   G+IY+    ++I  P+DAI+ GI  + EDRK  GL + MS+  N++L ++  
Sbjct: 318 FGADPVSSGQIYLGETELKITCPVDAIKHGIAYLSEDRKSHGLAINMSLASNITLTNMPA 377

Query: 359 IK-KGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILI 417
           +  +  FI F +E+  A   I    I+     + V  LSGGNQQK+V+AKWL    +IL 
Sbjct: 378 VTDRFGFIKFGQEETAAQTYIDALGIKTPSTQKIVKNLSGGNQQKIVIAKWLFRGSRILF 437

Query: 418 LDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIID 477
            DEPTRGIDVGAK  IY+++ +LA +G+GV+MISSELPE+L M+DR+AV   GK+A I++
Sbjct: 438 FDEPTRGIDVGAKFAIYQLLDELAAKGIGVVMISSELPEILGMTDRVAVFHEGKIAVILN 497

Query: 478 AKEASQEKVMKLAAG 492
            +E SQE++M  A+G
Sbjct: 498 TRETSQEEIMHHASG 512



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 54/218 (24%), Positives = 107/218 (49%), Gaps = 8/218 (3%)

Query: 30  GEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPSEAINAGIVTVFQELS 89
           GE+    G  GAG++ + + I G      G+I      ++   P +AI  GI  + ++  
Sbjct: 297 GEILGFAGLIGAGRTEVARAIFGADPVSSGQIYLGETELKITCPVDAIKHGIAYLSEDRK 356

Query: 90  ---VMDNLSVAENIFMGDEEK---RGIFIDYKKMYREAEKFMKEEFGIEIDPEEKLGK-Y 142
              +  N+S+A NI + +      R  FI + +    A+ ++ +  GI+    +K+ K  
Sbjct: 357 SHGLAINMSLASNITLTNMPAVTDRFGFIKFGQEETAAQTYI-DALGIKTPSTQKIVKNL 415

Query: 143 SIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVVKSLKEKGVAIIFISHRLE 202
           S   QQ + IA+ +++ +++L  DEPT  +       +++++  L  KG+ ++ IS  L 
Sbjct: 416 SGGNQQKIVIAKWLFRGSRILFFDEPTRGIDVGAKFAIYQLLDELAAKGIGVVMISSELP 475

Query: 203 EIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           EI  + D+V+V  +G+     +    ++E+I+    GR
Sbjct: 476 EILGMTDRVAVFHEGKIAVILNTRETSQEEIMHHASGR 513


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: 704
Number of extensions: 33
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: 518
Length adjustment: 34
Effective length of query: 460
Effective length of database: 484
Effective search space:   222640
Effective search space used:   222640
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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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