GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Sinorhizobium meliloti 1021

Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate SMc02739 SMc02739 glycine betaine transport ATP-binding ABC transporter protein

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



>FitnessBrowser__Smeli:SMc02739
          Length = 349

 Score =  246 bits (628), Expect = 5e-70
 Identities = 135/274 (49%), Positives = 185/274 (67%), Gaps = 8/274 (2%)

Query: 1   MSNAAISKIEVKNVFKIFGNRSKEALELIRQNKTKDQVLAETGCVVGVNDLSLSIGTGEI 60
           MS+A +     KNV  IFG   + A++++ Q KT+D++ A TG V+GV   SL+I  GEI
Sbjct: 1   MSDAVV----FKNVDIIFGKNPQLAVQMVDQGKTRDEIGAATGLVLGVAGASLTINEGEI 56

Query: 61  FVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGED----ILQLDMDALREFRRHKISMVF 116
            V+MGLSGSGKSTL+R  N L     G + V   +      + +  +LR+FR H +SMVF
Sbjct: 57  LVLMGLSGSGKSTLLRAVNGLAPVVRGEVEVKTANGSLNPYRCNAKSLRDFRMHTVSMVF 116

Query: 117 QSFGLLPHKSVLDNVAYGLKVRGESKQVCAERALHWINTVGLKGYENKYPHQLSGGMRQR 176
           Q F LLP ++V DNV +GL++ G +     +R    +  V L  + ++  ++LSGGM+QR
Sbjct: 117 QQFALLPWRTVADNVGFGLELAGVADAERRKRVGEQLELVNLAKWADRKVNELSGGMQQR 176

Query: 177 VGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTLHKTIVFITHDLDEAVRIG 236
           VGLARA A    I+LMDE FSALDPLIR  +QD+LLE Q+ L KTI+F++HDLDEA RIG
Sbjct: 177 VGLARAFATGAPILLMDEPFSALDPLIRTRLQDELLEFQRRLKKTIIFVSHDLDEAFRIG 236

Query: 237 NRIAILKDGKLIQVGTPREILHSPADEYVDRFVQ 270
           NRIAI++ G++IQ GTP+EI+  PA++YV  FVQ
Sbjct: 237 NRIAIMEGGRIIQCGTPQEIVKKPANQYVADFVQ 270


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: 271
Number of extensions: 11
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: 349
Length adjustment: 27
Effective length of query: 249
Effective length of database: 322
Effective search space:    80178
Effective search space used:    80178
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 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