Alignments for a candidate for xylG in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Phyllobacterium brassicacearum STM 196

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_106709787.1 CU102_RS04475 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_003010955.1:WP_106709787.1
          Length = 514

 Score =  419 bits (1076), Expect = e-121
 Identities = 226/498 (45%), Positives = 331/498 (66%), Gaps = 8/498 (1%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           +P+L ++++ K F  V AL  V+     GEVHA+ GENGAGKSTLM IIAGV QPDEGEI
Sbjct: 3   EPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGEI 62

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGD-EEKRGIFIDYKKMYRE 120
           + +G+ VR   P+ A + G+  V QE+++  + SVAENIFM     +R + ++Y+K+ RE
Sbjct: 63  VLDGKTVRIGSPAAAQSLGLGLVHQEIALCPDASVAENIFMASISRQRSLLMNYRKLERE 122

Query: 121 AEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKL 180
           A+  M       ID   K+G+  I+ QQ+VEIA+A+    +VLI DEPT++LT+ E   L
Sbjct: 123 AQAVMSRL--APIDVRRKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTEAEARIL 180

Query: 181 FEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240
           FE+++ LK  G++I++ISHR+ EIFE+CD+V+VLRDG Y+ TD + +LT + +V  MVGR
Sbjct: 181 FEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVVRRMVGR 240

Query: 241 KLEKFYIKE---AHEPGEVVLEVKNL-SGERFENVSFSLRRGEILGFAGLVGAGRTELME 296
           ++ + Y  +      P EVV  V+ L   ERF +V   L RGEILG  GL+G+GRTE+ E
Sbjct: 241 EITQLYPPKQPAGERPQEVVFSVRGLGDNERFRDVDIDLTRGEILGIGGLIGSGRTEIAE 300

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
            I G R    G+I I GK+  I    DA++ G+  + EDRK  GL L +SI  N+S+ +L
Sbjct: 301 GICGLRATTNGQILIHGKQQAIGTYADAVKAGLVYLSEDRKGSGLFLDLSIAKNISVLNL 360

Query: 357 DRIKKG-PFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKI 415
           D +      I    E +LA    +  +IR       V  LSGGNQQKV +AK LA++PK+
Sbjct: 361 DALTGHLGLIDTVGEGDLARDFAQRLNIRMGSIGAPVSSLSGGNQQKVAIAKQLAIQPKV 420

Query: 416 LILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGI 475
           +++DEPTRGIDVGAK+EI+ ++ +LA+ G+G+I+ISSELPE+L + DR+ V+  G++AG 
Sbjct: 421 ILMDEPTRGIDVGAKSEIHALLRELAQSGIGIIVISSELPELLGLCDRVIVIREGEVAGE 480

Query: 476 IDAKEASQEKVMKLAAGL 493
           +   + ++E+V++LA+G+
Sbjct: 481 LGMDDMTEERVIRLASGV 498



 Score =  102 bits (255), Expect = 2e-26
 Identities = 71/247 (28%), Positives = 120/247 (48%), Gaps = 15/247 (6%)

Query: 255 EVVLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEI 309
           E VL ++N++      +   NV+F+L RGE+    G  GAG++ LM  I G      GEI
Sbjct: 3   EPVLSIRNVTKHFGAVKALTNVNFALERGEVHALCGENGAGKSTLMNIIAGVLQPDEGEI 62

Query: 310 YIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK--GPFISF 367
            ++GK V I  P  A   G+GLV ++   + L    S+  N+ + S+ R +     +   
Sbjct: 63  VLDGKTVRIGSPAAAQSLGLGLVHQE---IALCPDASVAENIFMASISRQRSLLMNYRKL 119

Query: 368 KREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDV 427
           +RE +     +   D+R     RKV  L   +QQ V +AK L L  ++LI DEPT  +  
Sbjct: 120 EREAQAVMSRLAPIDVR-----RKVGELPISSQQLVEIAKALTLDCRVLIFDEPTAALTE 174

Query: 428 GAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVM 487
                ++ I+  L   G+ ++ IS  + E+ ++ DR+ V+  G+        + + + V+
Sbjct: 175 AEARILFEIIRDLKANGISIVYISHRMAEIFELCDRVTVLRDGRYVSTDRVADLTPDDVV 234

Query: 488 KLAAGLE 494
           +   G E
Sbjct: 235 RRMVGRE 241


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: 683
Number of extensions: 37
Number of successful extensions: 9
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: 514
Length adjustment: 34
Effective length of query: 460
Effective length of database: 480
Effective search space:   220800
Effective search space used:   220800
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