GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Rhizobium freirei PRF 81

Align ABC transporter for Lactose, permease component 1 (characterized)
to candidate WP_037152734.1 RHSP_RS17900 sugar ABC transporter permease

Query= reanno::Smeli:SM_b21653
         (298 letters)



>NCBI__GCF_000359745.1:WP_037152734.1
          Length = 308

 Score =  157 bits (397), Expect = 3e-43
 Identities = 98/300 (32%), Positives = 171/300 (57%), Gaps = 11/300 (3%)

Query: 1   MVRARRGIGRYYDVNGW---LFVAPALGLITLFMVYPIAWSLWMSFQSGRGM-TLKFAGF 56
           + R R    +++   GW    F+ P L  I LF+V PI  S+ +SF + + + T +F GF
Sbjct: 9   IARPRPRSRKWFRGEGWTALFFLLPGLIGIVLFLVLPILASIALSFTNWQLLGTPRFVGF 68

Query: 57  ANIVRLWN-DPVFIKALTNTMTYFVVQVPIMILLALILASLLNNPRLVGRGVFRTAIFLP 115
           +N +RL+  DP F   L NT+ + V  + + I+++L LA+ +++ + +G+  FR   FLP
Sbjct: 69  SNYLRLFTTDPQFWTVLRNTLFFTVEYLVLNIVISLGLATWISSLK-IGQRWFRVIFFLP 127

Query: 116 CVSSLVAYSVLFKGMFATDGIVNSTLQAIGLAASPIPWLTHPFWAKVLVILAITWRWTGY 175
             + L+A ++++  +F + G+ ++ + A+ L  S +  L     A   V+L   W   GY
Sbjct: 128 TFTPLIAVAMVWMLIFTSGGLFDNLMAALSLPFSGV--LNDRALAMQAVVLTSIWAGVGY 185

Query: 176 NMIFYLAALQNIDKSIYEVARIDGVPAWARLTHLTIPLLKPVILFTTVISTIGTLQLFDE 235
           N + + AAL  +  +  E ARIDG  AW R   + +PL+ P + F TV++ I +LQ+FD+
Sbjct: 186 NTVLFNAALDMVPATYLEAARIDGATAWDRFWKIRLPLISPTLFFGTVMTAITSLQVFDQ 245

Query: 236 VYNLTEGKGGPSNATLTLSLYIYNLTFRFMPNLGYAATVSYVIVVLVALLAFVQFFAARE 295
           ++ +T  KGGP ++T TL   IY   F+    +GYA+ +++V+  L+  L  +QF+  R+
Sbjct: 246 IFVMT--KGGPGSSTATLGYAIYQRGFQNF-QMGYASAIAWVMFALIMALTALQFWFQRK 302


Lambda     K      H
   0.330    0.142    0.447 

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: 306
Number of extensions: 19
Number of successful extensions: 6
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: 298
Length of database: 308
Length adjustment: 27
Effective length of query: 271
Effective length of database: 281
Effective search space:    76151
Effective search space used:    76151
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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