Alignments for a candidate for xylG in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Tistlia consotensis USBA 355

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_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  343 bits (879), Expect = 1e-98
 Identities = 189/490 (38%), Positives = 293/490 (59%), Gaps = 7/490 (1%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+LE++ + +RFPGV AL  V  +  PGEVH + GENGAGKST++ +IAG  +P EGE  
Sbjct: 22  PLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFR 81

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
           + G  V  N    A   GI  VFQE S++  ++V EN+F+G E  R   +D + ++  A+
Sbjct: 82  FRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRAD 141

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             +K   G  + P +++   + A QQMVEIA+A   +  VLILDEPT+SLT++ET +LF+
Sbjct: 142 AILKR-LGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFK 200

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +++ +K +GV +I+I+HRL EI  I D+++VLRDG Y+ T   +   + ++V +M GR  
Sbjct: 201 LIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRVY 260

Query: 243 EKFYIKEAHEPGEVVLEVKNL---SGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299
           ++ + K   +PG  +L V+ L   SG   E  S S+  GEI+G AGLVG+G++E+    F
Sbjct: 261 DELFPKVRFKPGRELLSVERLTTASGSVVE-ASLSVCAGEIVGLAGLVGSGKSEVARACF 319

Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLD-- 357
           G      G + ++G+ V    P   +++G   VP DR+  GL+++  +  NVSLPSL   
Sbjct: 320 GLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLA 379

Query: 358 RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILI 417
               G  +  + E +      +  +++P   +R V   SGGNQQKV+LAK      ++  
Sbjct: 380 PFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFA 439

Query: 418 LDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIID 477
            DEPT G+DVG +  IY  +  L + G G+++ISS+LPEVL +S+R  V   G++   + 
Sbjct: 440 FDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELA 499

Query: 478 AKEASQEKVM 487
             E ++EKV+
Sbjct: 500 GDEITEEKVL 509



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 72/246 (29%), Positives = 125/246 (50%), Gaps = 13/246 (5%)

Query: 253 PGEVVLEVKNLSGERF------ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRG 306
           P   +LE++ +S  RF      + V F LR GE+    G  GAG++ ++  I G      
Sbjct: 19  PAAPLLELRGVS-RRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSE 77

Query: 307 GEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFIS 366
           GE    G+ VE+N    A   GI  V ++     L+  M++  N+ L + +  + G  + 
Sbjct: 78  GEFRFRGEPVELNSVHHARGLGISAVFQE---FSLVPQMTVEENLFLGA-ESTRLG-LLD 132

Query: 367 FKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGID 426
            +   + AD  +K     P  P  +VL+L+   QQ V +AK    +  +LILDEPT  + 
Sbjct: 133 RRALHDRADAILKRLGF-PLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLT 191

Query: 427 VGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKV 486
               A++++++ Q+  +GVGVI I+  L E+ ++ DRI V+  G+    +DA+   + ++
Sbjct: 192 ERETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGEL 251

Query: 487 MKLAAG 492
           ++L  G
Sbjct: 252 VRLMTG 257



 Score = 58.5 bits (140), Expect = 5e-13
 Identities = 53/243 (21%), Positives = 104/243 (42%), Gaps = 13/243 (5%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           KP  E+ S+ +      ++   S+    GE+  + G  G+GKS + +   G+ +  EG +
Sbjct: 270 KPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHV 329

Query: 62  IYEGRGVRWNHPSEAINAGIVTV---FQELSVMDNLSVAENIFMGD----EEKRGIFIDY 114
             +G  V    P   +  G   V    ++  +M    V EN+ +          G  +D 
Sbjct: 330 RLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDR 389

Query: 115 KKMYREAEKFMKEEFGIEIDP---EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSS 171
           +    E ++  +    + + P   E  +  +S   QQ V +A++  +  +V   DEPT  
Sbjct: 390 R---GETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVG 446

Query: 172 LTQKETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKE 231
           +       ++E ++ L E G  I+ IS  L E+  + ++  V   G      + + +T+E
Sbjct: 447 VDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQAELAGDEITEE 506

Query: 232 KIV 234
           K++
Sbjct: 507 KVL 509


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: 689
Number of extensions: 24
Number of successful extensions: 7
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: 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 Apr 09 2024. 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