GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Rhodanobacter denitrificans 2APBS1

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09610
         (276 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  151 bits (381), Expect = 2e-41
 Identities = 91/233 (39%), Positives = 134/233 (57%), Gaps = 7/233 (3%)

Query: 43  GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102
           G +  +  +SL+   G    ++G SGSGKST++R    L  P  G + VDG  + + D+ 
Sbjct: 22  GRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSDVL 81

Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLK-GY 161
            LR     ++  V Q  GL PH + L N+A   +  G +++   +RA        L  G 
Sbjct: 82  PLRR----RVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGV 137

Query: 162 ENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKT 221
             +YP +LSGG RQRV L RAL AD D +L+DE   ALDP++R E+QD+L ++   L KT
Sbjct: 138 LERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKT 197

Query: 222 IVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV--QRR 272
           ++ +THDL EA     R+ +L+ G ++Q GT R++   PAD +V+RFV  QRR
Sbjct: 198 VIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAAQRR 250


Lambda     K      H
   0.321    0.138    0.387 

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: 189
Number of extensions: 9
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: 276
Length of database: 255
Length adjustment: 25
Effective length of query: 251
Effective length of database: 230
Effective search space:    57730
Effective search space used:    57730
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.

Links

Downloads

Related tools

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