GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Sphingomonas koreensis DSMZ 15582

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Ga0059261_1321 Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Korea:Ga0059261_1321
          Length = 238

 Score =  106 bits (265), Expect = 4e-28
 Identities = 78/246 (31%), Positives = 108/246 (43%), Gaps = 21/246 (8%)

Query: 4   IEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSG 63
           I +RN+ K+FG  A                         L  V L I       +MG SG
Sbjct: 8   IRLRNITKVFGEGAT--------------------AFQALKGVDLDIAERDFVAVMGPSG 47

Query: 64  SGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVL 123
           SGKST +  +  L  PTSGE LF G  I  L        R + +  VFQ F L+     L
Sbjct: 48  SGKSTTMNILGCLDVPTSGEFLFKGVYIETLDRDQRALVRRKYLGFVFQGFNLLSRTNAL 107

Query: 124 QNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTD 183
           +NV      RG  K    E+GM  ++ VGL+ +    P +LSGG  QRV +ARA+     
Sbjct: 108 ENVELPLLYRGEDKKVRHELGMAALEKVGLADWWDHTPAELSGGQPQRVAIARAIVTSPA 167

Query: 184 VILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVV 243
           V+L DE    LD     ++ + L  L ++   T++ +TH+ D A      I   +DG V 
Sbjct: 168 VLLADEPTGNLDSARSVEIMELLTSLNKDSGITVLMVTHEPDMA-AFARTIVHFKDGLVE 226

Query: 244 QVGTPN 249
           +    N
Sbjct: 227 RTEAGN 232


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: 163
Number of extensions: 13
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: 238
Length adjustment: 24
Effective length of query: 251
Effective length of database: 214
Effective search space:    53714
Effective search space used:    53714
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 17 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