GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metC in Escherichia coli BW25113

Align kynurenine-oxoglutarate transaminase (EC 2.6.1.7) (characterized)
to candidate 14737 b0600 putative aminotransferase (NCBI)

Query= BRENDA::Q71RI9
         (455 letters)



>FitnessBrowser__Keio:14737
          Length = 386

 Score =  212 bits (539), Expect = 2e-59
 Identities = 132/404 (32%), Positives = 209/404 (51%), Gaps = 30/404 (7%)

Query: 45  RIEGLDSNVWVEFTKLAADPSVVNLGQGFPDISPPSYVKEELSKAAFIDNMNQYTRGFGH 104
           ++  L + ++ + + LA     +NL QGFPD   P Y++E L+        NQY    G 
Sbjct: 11  KLPQLGTTIFTQMSALAQQHQAINLSQGFPDFDGPRYLQERLAHHV-AQGANQYAPMTGV 69

Query: 105 PALVKALSCLYGKIYQRQIDPNEEILVAVGAYGSLFNSIQGLVDPGDEVIIMVPFYDCYE 164
            AL +A++    ++Y  Q D + +I V  GA  +L+ +I  LV  GDEVI   P YD Y 
Sbjct: 70  QALREAIAQKTERLYGYQPDADSDITVTAGATEALYAAITALVRNGDEVICFDPSYDSYA 129

Query: 165 PMVRMAGAVPVFIPLRSKPTDGMKWTSSDWTFDPRELESKFSSKTKAIILNTPHNPLGKV 224
           P + ++G +   + L+  P   + W         +E  +  S +T+ +ILNTPHNP   V
Sbjct: 130 PAIALSGGIVKRMALQP-PHFRVDW---------QEFAALLSERTRLVILNTPHNPSATV 179

Query: 225 YTRQELQVIADLCVKHDTLCISDEVYEWLVYTGHTHVKIATLPGMWERTITIGSAGKTFS 284
           + + +   +      H+   ISDEVYE + ++   H  +   P + ER + + S GKT+ 
Sbjct: 180 WQQADFAALWQAIAGHEIFVISDEVYEHINFSQQGHASVLAHPQLRERAVAVSSFGKTYH 239

Query: 285 VTGWKLGWSIGPAHLIKHLQTVQQNSFYTCATPLQAALAEAFWIDIKRMDDPECYFNSLP 344
           +TGWK+G+ + PA +   ++ V Q   ++  TP Q ALA+          +PE Y  +LP
Sbjct: 240 MTGWKVGYCVAPAPISAEIRKVHQYLTFSVNTPAQLALADML------RAEPEHYL-ALP 292

Query: 345 KELEVKRDRMVRLLNSVGLKPIVPDGGYFIIADVSSLGADLSDMNSDEPYDYKFVKWMTK 404
                KRD +V  LN   L+ +  +G YF++ D S+    +S ++     D +F +W+T+
Sbjct: 293 DFYRQKRDILVNALNESRLEILPCEGTYFLLVDYSA----VSTLD-----DVEFCQWLTQ 343

Query: 405 HKKLTAIPVSAFCDSKSKPHFEKLVRFCFIKKDSTLDAAEEIFR 448
              + AIP+S FC   + P   KL+R CF KK+STL AA E  R
Sbjct: 344 EHGVAAIPLSVFC---ADPFPHKLIRLCFAKKESTLLAAAERLR 384


Lambda     K      H
   0.320    0.136    0.419 

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: 417
Number of extensions: 17
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: 455
Length of database: 386
Length adjustment: 32
Effective length of query: 423
Effective length of database: 354
Effective search space:   149742
Effective search space used:   149742
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: 50 (23.9 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