GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisM in Acidovorax caeni R-24608

Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate WP_054254771.1 BN2503_RS00920 ABC transporter permease subunit

Query= reanno::pseudo5_N2C3_1:AO356_05505
         (236 letters)



>NCBI__GCF_001298675.1:WP_054254771.1
          Length = 237

 Score =  178 bits (451), Expect = 9e-50
 Identities = 98/221 (44%), Positives = 145/221 (65%), Gaps = 12/221 (5%)

Query: 22  GLAMTLWLLSASLLIGFVVSIPLSIARVSPKFYVRWPVQFYTYLFRGTPLYIQLLICYTG 81
           GL +TL L   SL +G V+++  ++A VSP+ ++RWP Q +TY  RGTPL IQ+ + Y G
Sbjct: 18  GLVVTLQLTLYSLGLGAVLALACALALVSPRVWLRWPAQTFTYFMRGTPLLIQVYLIYYG 77

Query: 82  IYSIAAVRAQ-----PMLDSFFRDAMNCTILAFALNTCAYTTEIFAGAIRSMNHGEVEAA 136
           +  +  V+A+     P     F++   CT+L+F+LNT AYT E  AG+IR  N GEVEAA
Sbjct: 78  VAQLEWVQARWDAVWPWTQ--FKEPFFCTLLSFSLNTAAYTAETLAGSIRETNKGEVEAA 135

Query: 137 KAYGLTGWKLYAYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATVPDVLKVARDAN--- 193
           +A G+    L   +++PSA+RR LP Y NEV++MLHS+++A  +TVP +L +   A+   
Sbjct: 136 RAMGMGHGMLMRRIVLPSAIRRMLPAYGNEVVMMLHSSSLA--STVPALLDLTGAASRVY 193

Query: 194 SATFLTFQSFGIAALIYLTVTFALVGLFRLAERRWLAFLGP 234
           +  FL F+++  AA IYL +TFAL+G  +L ERR+L +L P
Sbjct: 194 ADFFLPFEAYLFAAAIYLCITFALIGASKLLERRFLGYLAP 234


Lambda     K      H
   0.329    0.140    0.433 

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: 8
Number of successful extensions: 3
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: 236
Length of database: 237
Length adjustment: 23
Effective length of query: 213
Effective length of database: 214
Effective search space:    45582
Effective search space used:    45582
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