GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Pseudomonas litoralis 2SM5

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_090274562.1 BLU11_RS14500 ATP-binding cassette domain-containing protein

Query= TCDB::Q9KKE1
         (275 letters)



>NCBI__GCF_900105005.1:WP_090274562.1
          Length = 260

 Score =  144 bits (364), Expect = 1e-39
 Identities = 97/263 (36%), Positives = 147/263 (55%), Gaps = 18/263 (6%)

Query: 23  MVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSG 82
           M    L+  ++  R G    L  V L    G +  I+G SGSGKSTL+R I+ L  P  G
Sbjct: 1   MTPPALEVRNLHKRYGDLEVLKGVDLLARDGDVISILGSSGSGKSTLLRCIDLLENPHRG 60

Query: 83  EVLFDGDNI-LDLG-------AKALRAFRMR-RVSMVFQSFALMPHRTVLQNVVYG-QRV 132
           ++L  G+ + L  G       A + +  R+R RV  VFQSF L PH ++L N++   +RV
Sbjct: 61  QILVAGEELKLKAGRDGALVAADSKQINRLRARVGFVFQSFNLWPHMSILDNIIEAPRRV 120

Query: 133 RGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFS 192
            G SK DA      +++ VG++     FP QLSGG +QR  +AR LA    VIL DE  S
Sbjct: 121 LGQSKVDAIAAAEVFLEKVGIADKMHAFPAQLSGGQQQRAAIARTLAMQPQVILFDEPTS 180

Query: 193 ALDPLIRGDMQDQLLQLQRNLA---KTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPN 249
           ALDP    +M  ++L + R LA   +T++ +TH+L  A ++ S++  L  GQV ++GTP+
Sbjct: 181 ALDP----EMVHEVLMVIRALADEGRTMLLVTHELGFARQVSSQVVFLHQGQVEEIGTPD 236

Query: 250 DILDNPANDYVARFVQRRHERPQ 272
            + D+P ++   +F+   H++ Q
Sbjct: 237 QVFDDPKSERCKQFMS-SHKKEQ 258


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: 202
Number of extensions: 17
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: 275
Length of database: 260
Length adjustment: 25
Effective length of query: 250
Effective length of database: 235
Effective search space:    58750
Effective search space used:    58750
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