GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03055 in Hafnia paralvei ATCC 29927

Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate WP_008812970.1 M988_RS12725 arginine ABC transporter substrate-binding protein

Query= reanno::pseudo3_N2E3:AO353_03055
         (258 letters)



>NCBI__GCF_001655005.1:WP_008812970.1
          Length = 243

 Score =  171 bits (434), Expect = 1e-47
 Identities = 98/251 (39%), Positives = 150/251 (59%), Gaps = 10/251 (3%)

Query: 1   MKKLVLLGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60
           MKK+++  A  L+ +S+   A E  ++   EA+YPPF     +  + GFD D+ NA+C++
Sbjct: 1   MKKIII--ATVLAGISVSASAAET-IRFAAEASYPPFEFMDANNQMQGFDIDLANAICKQ 57

Query: 61  MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGT 120
           MK  C +  Q FD LIP+LK ++IDA++S M IT +R+K V FT  YY+  A  + + G 
Sbjct: 58  MKATCTFTNQSFDSLIPSLKFKRIDAVISGMDITPERQKQVAFTAPYYDNSALFIAEKG- 116

Query: 121 QVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180
           +V+D +A LKGK++G+Q GS H ++ +E  K       PY S     LD+  GRLD    
Sbjct: 117 KVAD-IAALKGKRVGMQNGSTHQKYLQE--KHPEITPVPYDSYQNAILDLKNGRLDAVFG 173

Query: 181 DATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRAN 240
           D  ++++ +LK +S      VG   TD  YFG G+GIAVR+ +   L++ NAA+  ++ +
Sbjct: 174 DTAVVNE-WLKQNS--ALTAVGDKVTDPNYFGTGLGIAVRQNNAELLNQFNAALNQLKQD 230

Query: 241 GKYKQIQDKYF 251
           G YK I  K+F
Sbjct: 231 GTYKTIYSKWF 241


Lambda     K      H
   0.318    0.138    0.395 

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: 181
Number of extensions: 6
Number of successful extensions: 4
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: 258
Length of database: 243
Length adjustment: 24
Effective length of query: 234
Effective length of database: 219
Effective search space:    51246
Effective search space used:    51246
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: 46 (22.3 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