GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Chlorobium phaeobacteroides BS1

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate 642684274 Cphamn1_1781 L-alanine aminotransferase apoenzyme (EC 2.6.1.2)

Query= curated2:A8HZS2
         (378 letters)



>IMG__ChlphaBS1_FD:642684274
          Length = 405

 Score = 75.9 bits (185), Expect = 2e-18
 Identities = 56/176 (31%), Positives = 86/176 (48%), Gaps = 11/176 (6%)

Query: 84  KAMGID--PDRIICGAGSDEILNLIAHAYVGPGDEAIHCAHGFLVYK--IATLGAGGVPV 139
           +  GID  PD II  +G+ E  +L+  A + PGDE +  + G+ +Y   IA L A  +P 
Sbjct: 91  RCRGIDTTPDNIIVTSGASEAADLVCTAMLNPGDEVLCPSPGYPLYSAIIAKLNARELPY 150

Query: 140 VVPDREDLQMDVDAIIGAVTERTRVIFLANPNNPTGTYLPFNEVRRL-HAALPPNVLLVL 198
            +        D + I   +T RT+++ + NPNNPTG   P N +R L   A    +L++ 
Sbjct: 151 KLDPENSWLPDPEDIERRITSRTKILVVINPNNPTGELYPLNVLRSLADIARRHRLLIIS 210

Query: 199 DAAYSEYVRRNDYETGLELALSAEN---VIMCRTFSKIHGLAALRIGWAVASEAVI 251
           D  Y + V     E  + LA  AE+   +I   + SK       RIGW   + +V+
Sbjct: 211 DEVYHKLVYE---EVHIPLASLAEDDVAIITIDSLSKNLMAPGWRIGWLAITNSVL 263


Lambda     K      H
   0.318    0.134    0.393 

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: 356
Number of extensions: 16
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: 378
Length of database: 405
Length adjustment: 31
Effective length of query: 347
Effective length of database: 374
Effective search space:   129778
Effective search space used:   129778
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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