GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Hafnia paralvei ATCC 29927

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_004095864.1 M988_RS12735 arginine ABC transporter permease ArtM

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



>NCBI__GCF_001655005.1:WP_004095864.1
          Length = 222

 Score =  151 bits (382), Expect = 9e-42
 Identities = 82/220 (37%), Positives = 138/220 (62%), Gaps = 3/220 (1%)

Query: 8   IWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPM 67
           ++E +P    GL T+L L  +SLL  L+ AL   ++   +  ++      Y  +  GTP+
Sbjct: 1   MFEYIPDIIQGLPTSLSLTIISLLVALVLALLFTIVLTLRPVVLTQLVQGYITLFTGTPL 60

Query: 68  LVQLFLIYYGLAQFEAVRES-FLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNG 126
           LVQ+FLIYYG  QF+ ++++ +LW  LS    CA +A A+N++AYT ++  G+++A P+G
Sbjct: 61  LVQIFLIYYGPGQFDWIKQTPWLWNMLSQPWLCAMVALALNSAAYTTQLFYGAVKAIPSG 120

Query: 127 EIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAART 186
           + ++ +A+GMSR +   RILLP A +RAL  YSNEV+++ ++TSLA  +TL+++ G ++ 
Sbjct: 121 QWQSCEALGMSRSQTL-RILLPFAFKRALSSYSNEVVLIFKSTSLAYTITLMEVMGYSQQ 179

Query: 187 VNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWLGY 226
           +  + Y     +  AGV YLC+  +L  + +M E R L +
Sbjct: 180 MYGRTY-DVMVFGAAGVIYLCVNGLLTLIMRMVERRALAF 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: 153
Number of extensions: 9
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 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