GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsB in Rhizobium freirei PRF 81

Align LacI family transcriptional regulator; SubName: Full=Ribose transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_004110580.1 RHSP_RS05955 sugar ABC transporter substrate-binding protein

Query= uniprot:A0A1N7UEH6
         (318 letters)



>NCBI__GCF_000359745.1:WP_004110580.1
          Length = 328

 Score =  261 bits (667), Expect = 2e-74
 Identities = 140/318 (44%), Positives = 208/318 (65%), Gaps = 12/318 (3%)

Query: 1   MKLPFAGRLLAVAVLAAASAALPLSSAFADDAAKPKVGLVMKSLANEFFVTMQDGAKTYQ 60
           +KL  AG L    VLA +    P   AFA  A KPKVGL+MKSL+NEFF  M+ GA  Y 
Sbjct: 20  LKLGLAGTL----VLALSCGVSP---AFA--AGKPKVGLIMKSLSNEFFKQMKAGADKYA 70

Query: 61  KEHAADFDMITNGIKNETDTSAQIDIVNQMILAKVNAIVIAPADSKALVTVLKKASDAGI 120
            E+   FD    G+K+E D +AQ+D V   +  K + IV+APADSKA+ T L KA  AG+
Sbjct: 71  AENKDKFDFKAVGMKDERDFAAQVDAVENFVTQKYDIIVVAPADSKAMATPLAKAVKAGV 130

Query: 121 KVVNIDNRLDPDVLKSKNLDIPFVGPDNRKGSKLVGDYLAKQLASGDKVGIIEGVPTTTN 180
           KV+NID  LD D  K+  +D+ F GPDN++G+KL GD LAK L  G KV I+EG P   N
Sbjct: 131 KVINIDVPLDADAKKAAGIDLAFFGPDNKEGAKLAGDALAKDLGPGAKVVILEGNPEADN 190

Query: 181 AQQRTAGYKDAMDAAGMKIVSTQSGNWEIDQGQKVASAMLSEYPDLKALLAGNDNMALGA 240
           A++R  G+ D++    ++++ +++ +WE ++   V +  L++Y +++ ++A ND+MALG 
Sbjct: 191 AKERKEGFVDSIKGGKLELLDSKTAHWETEEANTVMTNFLTKYKNIQGVMAANDSMALGV 250

Query: 241 VSAVRAAGKAGKVLVVGYDNIEAIKPMLQDGRVLATADQAAAQQAVFGIQNALKLVKGEK 300
           V A+ A+G++GK+ VVG+DNI  +KP+++DG++LAT +Q  A+ AV GI+  L+ + GEK
Sbjct: 251 VKALDASGQSGKIKVVGFDNIPPVKPLIKDGKMLATVEQYGAEMAVMGIKYGLRELGGEK 310

Query: 301 VDSKDGVIETPVELVLKK 318
                G ++T ++LV  K
Sbjct: 311 F---SGWVKTDIKLVTTK 325


Lambda     K      H
   0.314    0.130    0.349 

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: 300
Number of extensions: 13
Number of successful extensions: 1
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: 318
Length of database: 328
Length adjustment: 28
Effective length of query: 290
Effective length of database: 300
Effective search space:    87000
Effective search space used:    87000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 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