GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Klebsiella michiganensis M5al

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate BWI76_RS09505 BWI76_RS09505 arginine transporter permease subunit ArtM

Query= reanno::pseudo3_N2E3:AO353_03045
         (232 letters)



>FitnessBrowser__Koxy:BWI76_RS09505
          Length = 222

 Score =  141 bits (356), Expect = 9e-39
 Identities = 79/216 (36%), Positives = 132/216 (61%), Gaps = 3/216 (1%)

Query: 12  LPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQL 71
           LP    GL T+L L A S++  L+ +L   ++   K P++      Y  +  GTP+LVQ+
Sbjct: 5   LPELLKGLHTSLTLTAASIVVALILSLIFTIILTLKTPVLVWIVRGYITLFTGTPLLVQI 64

Query: 72  FLIYYGLAQFEAVRE-SFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEA 130
           FLIYYG  QF +++E   LW  +S    CA +A ++N++AYT ++  G++RA P+G+ ++
Sbjct: 65  FLIYYGPGQFPSLQEYPVLWHLISEPWLCALIALSLNSAAYTTQLFHGAIRAIPDGQWQS 124

Query: 131 AKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQ 190
             A+GMS+ K    ILLP A +RAL  YSNEV+++ ++TSLA  +TL+++ G ++ +  +
Sbjct: 125 CGALGMSK-KDTLAILLPYAFKRALSSYSNEVVLVFKSTSLAYTITLMEVMGHSQLLYGR 183

Query: 191 YYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGY 226
            Y     +  AG+ YL +  +L  L ++ EH+ L +
Sbjct: 184 TY-DVMVFGAAGIVYLVVNGLLTLLMRLIEHKALAF 218


Lambda     K      H
   0.329    0.139    0.427 

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: 138
Number of extensions: 11
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: 232
Length of database: 222
Length adjustment: 22
Effective length of query: 210
Effective length of database: 200
Effective search space:    42000
Effective search space used:    42000
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 17 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