GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Sinorhizobium meliloti 1021

Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SMc04455 SMc04455 thiamine pyrophosphate protein

Query= curated2:Q7U5G1
         (617 letters)



>FitnessBrowser__Smeli:SMc04455
          Length = 548

 Score =  258 bits (658), Expect = 6e-73
 Identities = 179/553 (32%), Positives = 272/553 (49%), Gaps = 42/553 (7%)

Query: 22  SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81
           +G   +++AL  +GV  I   PG + L + DAL+ A+    ++ ++ R E      ADA+
Sbjct: 3   TGGQLVVEALAANGVKRISCVPGESYLAVLDALYDAD----IEVVVCRQEGGAAMMADAW 58

Query: 82  ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141
            R TG+ G+C  T GPGATN   G+  A+ DSVPM++  GQV R A   +AFQE +    
Sbjct: 59  GRLTGEPGICMVTRGPGATNASAGLHVARQDSVPMILFIGQVQREAREREAFQEIEYRRA 118

Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFN------YVPV 195
              + K    + DPA +   V +AF +A SGRPGPV++ +P+D+  +         Y PV
Sbjct: 119 FTEVAKWVGEIDDPARIPEFVTRAFAVATSGRPGPVVLTLPEDMLTQSTEAPAARAYQPV 178

Query: 196 EPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQL 255
           E              P  + +A   +L+  A+RP+  +GG   SA +    +  AER+QL
Sbjct: 179 E------------SHPGPSQIAKLAELLSTAKRPIAILGGTRWSAESVAGFQSFAERWQL 226

Query: 256 PVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTG---KLD 312
           PV  +   +  FD       G +G+         + E DL++ VG RF +  +     +D
Sbjct: 227 PVGCSFRRQMLFDHLHPNYAGDVGIGINPSLAGEIREADLVLLVGGRFSEMPSSGYTLID 286

Query: 313 TFAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERIN 372
              PR  +VH   DP E+G+  + D+A+       +A +   +L  +AEP    W  R  
Sbjct: 287 VPYPRQTLVHVHPDPGELGRVYRPDLAIAASPRDFVAAL--SNLTPSAEPH---WSARTG 341

Query: 373 TWKDRY-PLTIPPAEGAIYPQEVLLA------VRDLAPDAIVTTDVGQHQMWAAQHLRNG 425
                Y   + PP +G   P +V +         +  P+ I T   G +  W  +  R  
Sbjct: 342 EMHAAYLKWSTPPEKG---PGDVQMGPIVNWLEANTGPETIFTNGAGNYATWLHRFHRFR 398

Query: 426 PRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKV 485
             G  ++   G+MG+G+PAA+ A+   PDR+VVC AGD   LM+ QE  T   Y LP+ V
Sbjct: 399 RYGTQAAPASGSMGYGLPAAVAAKHLHPDREVVCFAGDGCFLMHGQEFATAVRYELPIIV 458

Query: 486 VIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLA 545
           ++VNN   G +R  QE  Y  R SA+D+ N  PDF ALAR++G  G  +   E       
Sbjct: 459 LVVNNGIYGTIRMHQEREYPGRVSATDLTN--PDFAALARAYGGHGETVARTEEFAGAFL 516

Query: 546 AALQSPTPTMIDV 558
            A +S  P +I++
Sbjct: 517 RARESGKPAIIEI 529


Lambda     K      H
   0.320    0.136    0.414 

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: 934
Number of extensions: 54
Number of successful extensions: 7
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: 617
Length of database: 548
Length adjustment: 36
Effective length of query: 581
Effective length of database: 512
Effective search space:   297472
Effective search space used:   297472
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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