Alignments for a candidate for xylG in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Rhizobium leguminosarum 3841

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_011652016.1 RL_RS12630 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_000009265.1:WP_011652016.1
          Length = 513

 Score =  404 bits (1039), Expect = e-117
 Identities = 219/496 (44%), Positives = 317/496 (63%), Gaps = 6/496 (1%)

Query: 2   KPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEI 61
           KP L +  + K +PGV AL+G+S++  PGEV  +VGENGAGKSTLMKI+ GV  PD G I
Sbjct: 15  KPFLSLSGVGKTYPGVVALEGLSIDIMPGEVIGLVGENGAGKSTLMKILGGVIAPDRGAI 74

Query: 62  IYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRG---IFIDYKKMY 118
           + +G  +R+     +I +GI  V QEL++ +NL VA NIF+G E  +      +D  ++ 
Sbjct: 75  LLDGTELRFLTVESSIASGIAFVHQELNLFENLDVAANIFLGREPLKAGPLKLVDRNRL- 133

Query: 119 REAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETE 178
           R+  K + +  G     +  +   S+A QQMVEIA+A+   A+++I DEPTSSL   ETE
Sbjct: 134 RDMVKPLLKRVGAHFSADTPVASLSLAEQQMVEIAKALSINARLVIFDEPTSSLPLAETE 193

Query: 179 KLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMV 238
           +L  ++KSLK  G+++IFISHRL E+  + D+V VLRDG  +GT + +++  +++V++M+
Sbjct: 194 RLLSIIKSLKADGISVIFISHRLHEVERVADRVVVLRDGTLVGTLAKKDIGHDQMVKLMI 253

Query: 239 GRKLEKFYIKEAHEPGEVVLEVKNLSGERFEN--VSFSLRRGEILGFAGLVGAGRTELME 296
           GR L     K    PG V L+   +  E +    V   +R GEI+G AGLVG+GRTEL  
Sbjct: 254 GRVLAARTAKPQRSPGSVALKASGVRTEAYPGRPVDLEIRYGEIMGLAGLVGSGRTELAR 313

Query: 297 TIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSL 356
             FG     GG I  +G+++ ++   DA+ +GI LVPEDRK+ G++L   I  N++L  L
Sbjct: 314 VFFGIDRSYGGAILQDGRQIAVSSARDAVARGIFLVPEDRKRNGILLDFPIAQNITLADL 373

Query: 357 DRIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKIL 416
            ++     +S +RE+  A+       I+      +   LSGGNQQKVVLAKWL++ PK++
Sbjct: 374 PKLSSRFMLSAERERAAAEKQRVRLGIKAPSVSTRTGTLSGGNQQKVVLAKWLSMSPKVM 433

Query: 417 ILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII 476
           I DEPTRGID+GAK EIY +M  LA  GV ++MISS++ EV+ +SDRIAVM  G++AGI+
Sbjct: 434 IFDEPTRGIDIGAKNEIYGLMRALADAGVAILMISSDMEEVIGVSDRIAVMHEGQIAGIL 493

Query: 477 DAKEASQEKVMKLAAG 492
           +  E SQE V+ LA G
Sbjct: 494 EEDEISQESVLLLAVG 509



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 65/249 (26%), Positives = 129/249 (51%), Gaps = 17/249 (6%)

Query: 12  KRFPGVHALK--GVSMEFYPG----------EVHAIVGENGAGKSTLMKIIAGVYQPDEG 59
           +R PG  ALK  GV  E YPG          E+  + G  G+G++ L ++  G+ +   G
Sbjct: 265 QRSPGSVALKASGVRTEAYPGRPVDLEIRYGEIMGLAGLVGSGRTELARVFFGIDRSYGG 324

Query: 60  EIIYEGRGVRWNHPSEAINAGIVTVFQELS---VMDNLSVAENIFMGDEEKRGI-FIDYK 115
            I+ +GR +  +   +A+  GI  V ++     ++ +  +A+NI + D  K    F+   
Sbjct: 325 AILQDGRQIAVSSARDAVARGIFLVPEDRKRNGILLDFPIAQNITLADLPKLSSRFMLSA 384

Query: 116 KMYREAEKFMKEEFGIEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQ 174
           +  R A +  +   GI+      + G  S   QQ V +A+ +    KV+I DEPT  +  
Sbjct: 385 ERERAAAEKQRVRLGIKAPSVSTRTGTLSGGNQQKVVLAKWLSMSPKVMIFDEPTRGIDI 444

Query: 175 KETEKLFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIV 234
               +++ ++++L + GVAI+ IS  +EE+  + D+++V+ +G+  G    + +++E ++
Sbjct: 445 GAKNEIYGLMRALADAGVAILMISSDMEEVIGVSDRIAVMHEGQIAGILEEDEISQESVL 504

Query: 235 EMMVGRKLE 243
            + VG++++
Sbjct: 505 LLAVGKRVK 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: 639
Number of extensions: 34
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 494
Length of database: 513
Length adjustment: 34
Effective length of query: 460
Effective length of database: 479
Effective search space:   220340
Effective search space used:   220340
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 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