GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2554 in Rhizorhabdus wittichii RW1

Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit

Query= reanno::acidovorax_3H11:Ac3H11_2554
         (222 letters)



>NCBI__GCF_000016765.1:WP_012048835.1
          Length = 374

 Score = 96.3 bits (238), Expect = 7e-25
 Identities = 46/135 (34%), Positives = 83/135 (61%)

Query: 85  LLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTVVLPQAVV 144
           L P FV  + G  IY+ A+ +E+VRG +  + +GQ EA+R++G+S   ++R V++PQA+ 
Sbjct: 239 LTPEFVAVLWGSVIYASAFAAEIVRGGLDGVPRGQWEASRALGLSKRQSLRLVIVPQALR 298

Query: 145 RMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYLAIAVVYFILTGAT 204
            ++PP+ ++FI ++KNS L  ++   DL       I+ + + LE    + +V+F L  A 
Sbjct: 299 MIVPPMNSQFITILKNSTLALVVGYPDLNFVANTAINHTGQGLEGVAILMLVFFTLASAI 358

Query: 205 TLVLRRIELRLRAGG 219
           +L + R+  R++ GG
Sbjct: 359 SLAMNRLNARVQRGG 373



 Score = 26.9 bits (58), Expect = 5e-04
 Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 7/68 (10%)

Query: 22  TVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFILFFGLPQ 81
           ++ +T   ++L  + G+ + + R +    +   L   +V  +R  PL+VQL  LF+    
Sbjct: 82  SIALTLLIIVLSTMAGVPIALAR-HSGHMLARTLAGGFVDLVRNVPLVVQL--LFW---- 134

Query: 82  FGILLPAF 89
           +G++L AF
Sbjct: 135 YGVILMAF 142


Lambda     K      H
   0.328    0.143    0.412 

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: 205
Number of extensions: 10
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 222
Length of database: 374
Length adjustment: 26
Effective length of query: 196
Effective length of database: 348
Effective search space:    68208
Effective search space used:    68208
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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