GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Desulfitobacterium hafniense DCB-2

Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_015944380.1 DHAF_RS15445 diaminopimelate aminotransferase

Query= reanno::Putida:PP_0967
         (348 letters)



>NCBI__GCF_000021925.1:WP_015944380.1
          Length = 388

 Score = 79.7 bits (195), Expect = 1e-19
 Identities = 83/252 (32%), Positives = 120/252 (47%), Gaps = 20/252 (7%)

Query: 85  GSDEVLAHIFHGLFQHDAPLLFPDISYSFYPVYCGLYGIAFEQVALDEQFQ-------IR 137
           GS + LAHIF  L       L PD  Y  Y    GL     E+VAL  + +         
Sbjct: 99  GSQDGLAHIFLALCDPGDVALIPDPGYPIYTA--GLVLAGGEKVALPLREENGFLPDLSA 156

Query: 138 IEDYKKPNAGIIFPN-PNAPTGCLMPLQAVEELLQANRDSVVVV--DEAYID--FGGETA 192
           IED     A I+F N PN PT  + PL   EE++   R + +VV  D AY +  F G   
Sbjct: 157 IEDEVAQQAKIMFLNYPNNPTAAVAPLSFFEEVVDFARRNRIVVCHDAAYSELAFDGYRP 216

Query: 193 ISLVD---RYDNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFNSYPLDRAAI 249
           +S +      +  +   ++SK+ +LAG+R+G AVG+ ++I AL  +K++ +    + A  
Sbjct: 217 VSFLQVPGAKEVGIEFHSVSKTYNLAGVRLGFAVGNGEIIGALAELKSNIDYGVFEPALQ 276

Query: 250 VGAAVAFEDREYFEETCRKVIDSREVLV-GQLQAKGFEVLPSAANFIFARHP-QQDAGEL 307
            GA      +E  E+  R   + R++ V G  QA      P  + FI+A  P  QD+   
Sbjct: 277 AGAYALSASQENVEQNRRAYQERRDIWVKGCAQAGWSMPSPRGSMFIWAPVPTAQDSRSF 336

Query: 308 A-ARLREQGVIV 318
           A A  RE GVIV
Sbjct: 337 AFALAREAGVIV 348


Lambda     K      H
   0.321    0.139    0.408 

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: 340
Number of extensions: 22
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: 348
Length of database: 388
Length adjustment: 30
Effective length of query: 318
Effective length of database: 358
Effective search space:   113844
Effective search space used:   113844
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: 49 (23.5 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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