GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aceA in Escherichia coli BW25113

Align Bifunctional glyoxylate cycle protein; Gex-3-interacting protein 7; EC 4.1.3.1; EC 2.3.3.9 (characterized)
to candidate 18042 b4014 malate synthase (NCBI)

Query= SwissProt::Q10663
         (968 letters)



>FitnessBrowser__Keio:18042
          Length = 533

 Score =  495 bits (1275), Expect = e-144
 Identities = 263/513 (51%), Positives = 336/513 (65%), Gaps = 9/513 (1%)

Query: 453 DEKILTPDALRFLHDLNTEFNPRRLRLLSKRNQVQADINNSLWFPDFNKETEVLRSDQGW 512
           +++ILT +A+ FL +L T F P+R +LL+ R Q Q DI+N    PDF  ET  +R D  W
Sbjct: 21  EKQILTAEAVEFLTELVTHFTPQRNKLLAARIQQQQDIDNGT-LPDFISETASIR-DADW 78

Query: 513 KGAEIPRDLQDRRVEITGPTDRKMVINAMNSGANVFMADFEDSNSPTWRNQLEGQINLYD 572
           K   IP DL+DRRVEITGP +RKMVINA+N+   VFMADFEDS +P W   ++GQINL D
Sbjct: 79  KIRGIPADLEDRRVEITGPVERKMVINALNANVKVFMADFEDSLAPDWNKVIDGQINLRD 138

Query: 573 AVRNNISYTHPTTKKEYTLNEKHAVLKVRPRGWHLPEKHVLIHNQPTSGSLFDFGLFVFH 632
           AV   ISYT+   K  Y L    AVL  R RG HLPEKHV    +   GSLFDF L+ FH
Sbjct: 139 AVNGTISYTNEAGKI-YQLKPNPAVLICRVRGLHLPEKHVTWRGEAIPGSLFDFALYFFH 197

Query: 633 NAKALIAQGSGPYFYLPKLQSAEEAQLWADVFKYTEDKLGLARGTIKCTVLIEHLLASFQ 692
           N +AL+A+GSGPYFYLPK QS +EA  W++VF Y ED+  L RGTIK T+LIE L A FQ
Sbjct: 198 NYQALLAKGSGPYFYLPKTQSWQEAAWWSEVFSYAEDRFNLPRGTIKATLLIETLPAVFQ 257

Query: 693 LHEIIHALKDNIVGLNCGRWDYIFSYIKTFQNHRKFLLPDRFQIGMTAPFMRNYSLEVIK 752
           + EI+HAL+D+IVGLNCGRWDYIFSYIKT +N+   +LPDR  + M  PF+  YS  +IK
Sbjct: 258 MDEILHALRDHIVGLNCGRWDYIFSYIKTLKNYPDRVLPDRQAVTMDKPFLNAYSRLLIK 317

Query: 753 ACHLRGIHAMGGMAAQIPIKHDQVANDKAFALVRADKEREATDGHDGTWVAHPGLVPLAK 812
            CH RG  AMGGMAA IP K D+  N++    V+ADK  EA +GHDGTW+AHPGL   A 
Sbjct: 318 TCHKRGAFAMGGMAAFIPSK-DEEHNNQVLNKVKADKSLEANNGHDGTWIAHPGLADTAM 376

Query: 813 RVFDQMM-PKPNQISKNLTR-ANCTKEDLTVIPEGTRTEAGFRHNISVTLGYLDSWLRGT 870
            VF+ ++  + NQ+     + A  T + L    +G RTE G R NI V + Y+++W+ G 
Sbjct: 377 AVFNDILGSRKNQLEVMREQDAPITADQLLAPCDGERTEEGMRANIRVAVQYIEAWISGN 436

Query: 871 GCVPLYNLMEDAATAEISRAQLWQWLHHDAKLEDGRTIDAGLVKQTIAAETERRLIRAGS 930
           GCVP+Y LMEDAATAEISR  +WQW+HH   L +G+ +   L +Q +  E +      G 
Sbjct: 437 GCVPIYGLMEDAATAEISRTSIWQWIHHQKTLSNGKPVTKALFRQMLGEEMKVIASELGE 496

Query: 931 ---VVNRIPEAADLLEKFVTEEKMSDFLTTDAY 960
                 R  +AA L+E+  T +++ DFLT   Y
Sbjct: 497 ERFSQGRFDDAARLMEQITTSDELIDFLTLPGY 529


Lambda     K      H
   0.319    0.134    0.402 

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: 1200
Number of extensions: 49
Number of successful extensions: 6
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: 968
Length of database: 533
Length adjustment: 40
Effective length of query: 928
Effective length of database: 493
Effective search space:   457504
Effective search space used:   457504
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: 55 (25.8 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