GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Collimonas arenae Ter10

Align ABC transporter for L-Lysine, permease component 1 (characterized)
to candidate WP_061531811.1 CAter10_RS00190 amino acid ABC transporter permease

Query= reanno::pseudo5_N2C3_1:AO356_09905
         (231 letters)



>NCBI__GCF_001584165.1:WP_061531811.1
          Length = 218

 Score =  138 bits (348), Expect = 7e-38
 Identities = 81/218 (37%), Positives = 127/218 (58%), Gaps = 11/218 (5%)

Query: 8   FGPALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYSTLVRGIPELLW 67
           F P L  GA++TV++   +L L  VLGLL AL K S  +P+ W   ++  ++RG+P ++ 
Sbjct: 9   FLPILLRGAVVTVEVTFYSLILSTVLGLLLALMKLSQLRPVSWFAASFINIIRGLPIIVQ 68

Query: 68  VLLIYFGTVNLMRALGEYLGMPDLALNAFAAGVIALGLCFGAYATEVFRGAILAIPKGHR 127
           +  IYF    ++  LG       + L+AF AGVI LG+ +  Y  E FR  I A+  G  
Sbjct: 69  LFYIYF----VLPELG-------IQLSAFQAGVIGLGIAYSVYQAENFRAGIEAVDPGQI 117

Query: 128 EAGVALGLSKWRIFTRLIMPQMWRIALPGLGNLFMILMKDTALVSVIGLEEIMRHAQIGV 187
           EA  ++G+ +  I  R+++PQ +RIALP  GN  ++++KD++LVS I + E+ R  Q+  
Sbjct: 118 EAAQSIGMRRAMIMRRVVLPQAFRIALPPYGNTLVMMLKDSSLVSTITVLEMTRAGQMIA 177

Query: 188 TVSKQPFTFYMVAALMYLGLTVLAMLGMHLLERRAARG 225
           + + Q  T Y + ALMYL L++  +L    LE R  +G
Sbjct: 178 SSTFQNMTVYTMVALMYLLLSLPLVLLTRRLEARFGQG 215


Lambda     K      H
   0.329    0.143    0.435 

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: 148
Number of extensions: 10
Number of successful extensions: 2
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: 231
Length of database: 218
Length adjustment: 22
Effective length of query: 209
Effective length of database: 196
Effective search space:    40964
Effective search space used:    40964
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 (21.8 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