GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Ruegeria conchae TW15

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_010442422.1 G7G_RS0115845 glycine betaine/L-proline ABC transporter ATP-binding protein

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



>NCBI__GCF_000192475.1:WP_010442422.1
          Length = 342

 Score =  273 bits (697), Expect = 5e-78
 Identities = 143/268 (53%), Positives = 194/268 (72%), Gaps = 1/268 (0%)

Query: 3   NAAISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFV 62
           +A    I  +NV+K+FG   +  L+ +   ++ D++ A+ G + GV D+S+ +G GE+ V
Sbjct: 2   SATAPVISAQNVWKLFGPSPESYLKSMPAGRSFDEIRAD-GYIAGVKDVSIEVGRGEMLV 60

Query: 63  IMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLL 122
           IMGLSGSGKSTLVR F+RL D T G I VDG+DI+ L    L E RR+K+ MVFQSFGLL
Sbjct: 61  IMGLSGSGKSTLVRCFSRLHDITGGTIKVDGQDIMGLSERDLIELRRNKMGMVFQSFGLL 120

Query: 123 PHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARA 182
           PH++VLDNVA+ L++RG+ +    ERAL  I  VGL+G E  +P +LSGG +QRVG+AR+
Sbjct: 121 PHRTVLDNVAFPLEMRGQDRHDRRERALEVIKLVGLEGREEYFPRELSGGQQQRVGIARS 180

Query: 183 LAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAIL 242
           LA + DI  +DE FSALDPLIR EMQD+ L LQ+ L KTIVFITHD DEA+R+ +RIAI+
Sbjct: 181 LAIEPDIWFLDEPFSALDPLIRREMQDEFLRLQEMLGKTIVFITHDFDEALRLADRIAIM 240

Query: 243 KDGKLIQVGTPREILHSPADEYVDRFVQ 270
           ++G + Q  TP +I+ +PA EYV +F +
Sbjct: 241 RNGAVEQCDTPDQIVMNPATEYVAKFTE 268


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: 255
Number of extensions: 12
Number of successful extensions: 2
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: 342
Length adjustment: 27
Effective length of query: 249
Effective length of database: 315
Effective search space:    78435
Effective search space used:    78435
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: 48 (23.1 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