GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Mesorhizobium ciceri WSM1271

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate YP_004144287.1 Mesci_5138 glycine betaine/L-proline ABC transporter ATPase

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



>NCBI__GCF_000185905.1:YP_004144287.1
          Length = 361

 Score =  265 bits (677), Expect = 1e-75
 Identities = 134/263 (50%), Positives = 185/263 (70%), Gaps = 1/263 (0%)

Query: 8   KIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEIFVIMGLS 67
           K+  +NV+K+FG+ +   +   R  K     +   G V  V  + L I  GEIF+IMGLS
Sbjct: 22  KLACRNVWKLFGSNAANFIRE-RDGKASMADVTAAGLVGAVRAVDLEIRQGEIFIIMGLS 80

Query: 68  GSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMDALREFRRHKISMVFQSFGLLPHKSV 127
           GSGKSTLVR  +RL++PT G +  +G D+L++   AL E RRH++ MVFQ+F LLPH +V
Sbjct: 81  GSGKSTLVRCMSRLVEPTHGKVEFEGNDLLKISDAALIELRRHRMGMVFQNFALLPHLNV 140

Query: 128 LDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQRVGLARALAADT 187
           L+N+A+ L ++G+ +     RA   I  VGL+G E+ YP +LSGG +QRVG+AR+LA   
Sbjct: 141 LENIAFPLSIQGQDRATREARAREVIELVGLRGREHFYPRELSGGQQQRVGIARSLATKP 200

Query: 188 DIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIGNRIAILKDGKL 247
           +I  +DE FSALDPLIR EMQD+L+ LQ  LHKTIVFITHD DEA+R+ +RIAI+KDG++
Sbjct: 201 EIWFLDEPFSALDPLIRREMQDELMRLQMMLHKTIVFITHDFDEAIRLADRIAIMKDGEV 260

Query: 248 IQVGTPREILHSPADEYVDRFVQ 270
           IQ+GTP E++ +PA +YV  F +
Sbjct: 261 IQIGTPEELVVNPATDYVAEFTR 283


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: 272
Number of extensions: 12
Number of successful extensions: 1
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: 361
Length adjustment: 27
Effective length of query: 249
Effective length of database: 334
Effective search space:    83166
Effective search space used:    83166
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