GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylG in Rhodobacter viridis JA737

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_110805879.1 C8J30_RS10885 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>NCBI__GCF_003217355.1:WP_110805879.1
          Length = 511

 Score =  384 bits (987), Expect = e-111
 Identities = 216/477 (45%), Positives = 306/477 (64%), Gaps = 8/477 (1%)

Query: 5   LEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYE 64
           L ++   K +PG  ALKGV  +   G V+ +VGENGAGKSTLMK+IAGV    EG I  +
Sbjct: 9   LSIRGGVKVYPGTRALKGVDFDLRMGAVNVLVGENGAGKSTLMKLIAGVEDMTEGTITMD 68

Query: 65  GRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRG-IFIDYKKMYREAEK 123
           GR +R+   ++A+ AGI  VFQEL++  NLSVAENIF+G E  RG I ID +  +REA +
Sbjct: 69  GREMRFRTKADAVAAGIGIVFQELNLFPNLSVAENIFIGHETTRGGIDIDIEA-HREATR 127

Query: 124 FMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEV 183
            + E     I P+  LG   I  QQ+VEIA+A+ + A++LILDEPTS+L+  E E LF V
Sbjct: 128 QLMERLEQNIHPDTPLGNLRIGQQQIVEIAKALAQNARILILDEPTSALSAAEVEVLFRV 187

Query: 184 VKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKLE 243
           +  L  +GV I++ISHRLEE+  + D ++VLRDG   G  S+E +    IV+ M+G   +
Sbjct: 188 IDELTAQGVGIVYISHRLEELIRVGDYITVLRDGVITGARSMEGVDIPWIVKAMIGSSSK 247

Query: 244 KFYIKEAHEPGEVVLEVKNLS------GERFENVSFSLRRGEILGFAGLVGAGRTELMET 297
           ++   E    G  +   ++++      G   ++VS S+R GEI+G  GL+GAGR+E +E 
Sbjct: 248 EYGRSEVANFGPEIFRAEDITLPRAGGGFTVDHVSLSIRSGEIVGLYGLMGAGRSEFLEC 307

Query: 298 IFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLD 357
           +    P  GG+ ++EGK +        I +GI L+PEDRK+ GLI IMSI  N++L SL 
Sbjct: 308 VMAQHPHSGGKFWVEGKPLTERDVPGRIARGIALIPEDRKRDGLIQIMSIRENLTLSSLP 367

Query: 358 RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILI 417
              K   +  K+E + A   IK   I+ A P+  V  LSGGNQQKVV+ K L   PK+L+
Sbjct: 368 SFTKLFHLDLKKEAKTAVEFIKRLTIKVASPENPVSSLSGGNQQKVVIGKALMTGPKVLL 427

Query: 418 LDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAG 474
           +DEP+RGID+GAKAE++R M +LA EG+G++ ++S+L EVL +SDRI VM+ G++ G
Sbjct: 428 MDEPSRGIDIGAKAEVFRTMRRLAAEGLGILFVTSDLDEVLALSDRIIVMAQGRVTG 484


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: 659
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 494
Length of database: 511
Length adjustment: 34
Effective length of query: 460
Effective length of database: 477
Effective search space:   219420
Effective search space used:   219420
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:

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:

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:

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:

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