GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Rhodanobacter denitrificans 2APBS1

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  149 bits (375), Expect = 8e-41
 Identities = 92/238 (38%), Positives = 129/238 (54%), Gaps = 5/238 (2%)

Query: 36  RSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLG 95
           R G    L  VSL   AG    ++G SGSGKST++R +  L  P  G V  DG  +    
Sbjct: 20  RYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSD 79

Query: 96  AKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGL-S 154
              LR    RRV  V Q   L PH T L N+    R  G +++  R+   +      L +
Sbjct: 80  VLPLR----RRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPT 135

Query: 155 GYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLA 214
           G   ++P +LSGG +QRV L RAL AD D +L+DE   ALDP++R ++QD+L Q+   L 
Sbjct: 136 GVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLG 195

Query: 215 KTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQRRHERPQ 272
           KT++ +THDL EA      + +LR G V+Q GT  D+ + PA+ +V RFV  +   P+
Sbjct: 196 KTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAAQRRLPE 253


Lambda     K      H
   0.323    0.139    0.397 

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: 194
Number of extensions: 15
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: 275
Length of database: 255
Length adjustment: 25
Effective length of query: 250
Effective length of database: 230
Effective search space:    57500
Effective search space used:    57500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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