GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tpiA in Sinorhizobium meliloti 1021

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate SMc03981 SMc03981 phosphoglycerate kinase

Query= BRENDA::P36204
         (654 letters)



>FitnessBrowser__Smeli:SMc03981
          Length = 399

 Score =  364 bits (935), Expect = e-105
 Identities = 191/383 (49%), Positives = 254/383 (66%), Gaps = 2/383 (0%)

Query: 10  DLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69
           D+ GKRV++RVD NVPVKDG V D TRI    PTI+   E+GAKV+LL+H GRPKGEP  
Sbjct: 11  DIAGKRVLVRVDLNVPVKDGQVTDTTRIERVAPTIRELSEKGAKVVLLAHFGRPKGEPVA 70

Query: 70  EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129
           + SL  +A  + E+L + V F    +GD+   A+ EL +GEVLLLENTRFH GE KND +
Sbjct: 71  DMSLKAIASAVEEILDQRVYFAADCIGDKAANAIAELNDGEVLLLENTRFHKGEEKNDSD 130

Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPY 189
                A+  DI+VNDAF  AHRAHAS  G+A  +P+ AG  M+ E++ L K   NP++P 
Sbjct: 131 FVTALAANGDIYVNDAFSAAHRAHASTEGLAHHLPAYAGRTMQAELEALEKGLGNPKRPV 190

Query: 190 VVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKEL 249
           V ++GGAKVS KI ++ NL++K D ++IGG M  TFL A G +VG S  E D  + AK +
Sbjct: 191 VAIVGGAKVSTKIDLLQNLVKKVDALVIGGGMANTFLAAQGVDVGKSLCEHDLAETAKAI 250

Query: 250 LEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLS 309
           L  A E G  IVLPVD V+A++ + G + +VV I   IP   M LD+GP++IE   + +S
Sbjct: 251 LAAASEAGCAIVLPVDGVVAREFKAGADNEVVDI-KAIPADAMVLDVGPKSIEAINEWIS 309

Query: 310 DAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGA-ITVVGGGDSAAAVNKFGLEDK 368
            A+T+VWNGP+G FEI  F   T   A   AA T  G+ ++V GGGD+ AA+N   + D 
Sbjct: 310 RAETLVWNGPLGAFEIAPFDRATVAAAKHAAARTRAGSLVSVAGGGDTVAALNHAEVADD 369

Query: 369 FSHVSTGGGASLEFLEGKELPGI 391
           F++VST GGA LE++EGK LPG+
Sbjct: 370 FTYVSTAGGAFLEWMEGKPLPGV 392


Lambda     K      H
   0.317    0.137    0.386 

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: 583
Number of extensions: 26
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: 654
Length of database: 399
Length adjustment: 34
Effective length of query: 620
Effective length of database: 365
Effective search space:   226300
Effective search space used:   226300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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