Alignments for a candidate for xylG in Ochrobactrum thiophenivorans DSM 7216

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Ochrobactrum thiophenivorans DSM 7216

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_094506741.1 CEV31_RS09015 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_002252445.1:WP_094506741.1
          Length = 523

 Score =  401 bits (1031), Expect = e-116
 Identities = 218/495 (44%), Positives = 323/495 (65%), Gaps = 8/495 (1%)

Query: 4   ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63
           +L ++ + K + G+ A+K  ++E   G V+ +VGENGAGKSTLMKIIAGV +P  G+II 
Sbjct: 12  VLRLEDVSKVYSGIVAVKRANLELRRGSVNVLVGENGAGKSTLMKIIAGVERPTIGKIIL 71

Query: 64  EGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIF-IDYKKMYREAE 122
           +G  V ++ P++A   GI  +FQEL++  N+SVAENIF   E  RGI  ID+K   ++A 
Sbjct: 72  DGEEVSFDSPADAQKRGIAMIFQELNLFSNMSVAENIFAKREITRGIRGIDHKAQIKKAN 131

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           +++ +     ID    +    I  QQ+VEIA+A+   A+++I+DEPTS+L+  E + LF+
Sbjct: 132 EYL-DRLDAGIDARTMVADLPIGQQQLVEIAKAISIDARIVIMDEPTSALSAAEVDILFK 190

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           V+  LK +GVAI++ISHRLEE+  I D ++VLRDG+  G + I+N+  + IV  M+G   
Sbjct: 191 VIADLKSRGVAIVYISHRLEELMRIGDYITVLRDGQITGQEEIKNINTQWIVRSMIGSDA 250

Query: 243 EKFYIKEAHEPGEVVLEVKNLS------GERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           + F     H+ G  +   +N++      G   +NVS S+R GE+LG  GL+GAGR+E  E
Sbjct: 251 KDFAKAVTHKMGGEMFRAENITLPRAIGGLAVDNVSLSVRAGEVLGIYGLMGAGRSEFFE 310

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            I G      GEIYI+GK+V        I +G+ L+PEDR++ GL+ I+SI  N++L SL
Sbjct: 311 CIMGQHAHSTGEIYIDGKKVTERDTTRRIRRGLALIPEDRQREGLVQILSIASNLTLASL 370

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
           DR+ +   IS KREK+    AIK   I+   PD +V  +SGGNQQKVV+ K L   PK+L
Sbjct: 371 DRLARFFHISPKREKQAIQEAIKDLAIKAPNPDFEVTSMSGGNQQKVVIGKALMTNPKVL 430

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           ++DEP+RGIDVGAKA+++R M +LA EG+ ++  +S+L EV+ +SDRIAV+S GKL  I 
Sbjct: 431 LMDEPSRGIDVGAKADVFRTMRRLAGEGLAILFSTSDLEEVMALSDRIAVLSNGKLIAIF 490

Query: 477 DAKEASQEKVMKLAA 491
           D + A++  ++  +A
Sbjct: 491 DRENATEADIVAASA 505



 Score = 93.2 bits (230), Expect = 2e-23
 Identities = 65/252 (25%), Positives = 124/252 (49%), Gaps = 16/252 (6%)

Query: 249 EAHEPGEVVLEVKNLSGE-----RFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRP 303
           E H   ++VL ++++S         +  +  LRRG +    G  GAG++ LM+ I G   
Sbjct: 4   ETHNKDDIVLRLEDVSKVYSGIVAVKRANLELRRGSVNVLVGENGAGKSTLMKIIAGVER 63

Query: 304 KRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNV-SLPSLDRIKKG 362
              G+I ++G+ V  + P DA ++GI ++ ++   L L   MS+  N+ +   + R  +G
Sbjct: 64  PTIGKIILDGEEVSFDSPADAQKRGIAMIFQE---LNLFSNMSVAENIFAKREITRGIRG 120

Query: 363 --PFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDE 420
                  K+  E  D      D R    D  +     G QQ V +AK +++  +I+I+DE
Sbjct: 121 IDHKAQIKKANEYLDRLDAGIDARTMVADLPI-----GQQQLVEIAKAISIDARIVIMDE 175

Query: 421 PTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKE 480
           PT  +       ++++++ L   GV ++ IS  L E++++ D I V+  G++ G  + K 
Sbjct: 176 PTSALSAAEVDILFKVIADLKSRGVAIVYISHRLEELMRIGDYITVLRDGQITGQEEIKN 235

Query: 481 ASQEKVMKLAAG 492
            + + +++   G
Sbjct: 236 INTQWIVRSMIG 247


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: 676
Number of extensions: 37
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: 523
Length adjustment: 34
Effective length of query: 460
Effective length of database: 489
Effective search space:   224940
Effective search space used:   224940
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 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