GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Azospirillum brasilense Sp245

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AZOBR_RS10240 AZOBR_RS10240 L-threonine-O-3-phosphate decarboxylase

Query= curated2:A7MJP4
         (360 letters)



>FitnessBrowser__azobra:AZOBR_RS10240
          Length = 339

 Score = 94.7 bits (234), Expect = 3e-24
 Identities = 87/295 (29%), Positives = 134/295 (45%), Gaps = 32/295 (10%)

Query: 31  LNANEYPLPVEFQLTAQTLNRYPECQPKRVI-ERYAQYAGVKPEQVLVSRGADEGIELLI 89
           +N   YPLP    + A    R P    +  + E  A   GV     + + G  + +  ++
Sbjct: 38  INPWPYPLP---PIPADAWARLPGRAAETALREAAAACYGVPSADRVAAAGGSQALIQIL 94

Query: 90  RAFCEPGRDAVLYCPPTYGMYSVSAETSGVECRTVQATDGWQLDLPAIAEQLDGVKVIFV 149
                PG  AVL   PTY  ++     +G     V++ +G   D            V+ V
Sbjct: 95  PRLRRPGTVAVL--GPTYAEHAAGWAKAGHRVAEVESLEGCDAD------------VVVV 140

Query: 150 CSPNNPTGQLINPQDLRTLLEM--ARGKAIVVADEAYIEFCPQATLAGWLGEYPHLVVLR 207
            +PNNP G+++ P+ L  L E   ARG  +VV DEA+ E  P+ ++A   G    LV+LR
Sbjct: 141 VNPNNPDGRIVPPETLLALAERQAARGGWLVV-DEAFAEVTPECSVASEAGR-AGLVILR 198

Query: 208 TLSKAFALAGLRCGFTLANEEVINLLLKVIAPYPLSTPVADIAAQALSPEG-ITAMRERV 266
           +  K F LAG+R GF L    ++  L   + P+ +S P   IA  ALS    I A R R+
Sbjct: 199 SFGKFFGLAGVRLGFLLGEPALVRDLRAAVGPWAVSGPALTIATAALSDSAWIAATRRRL 258

Query: 267 AQVLANRD--VLIAGLRETPCVEAVFDSETNYVLARITASSAVFKSLWDQGIILR 319
           A   A  D  ++ AG+R       V    + + L     S+ ++K L   G+++R
Sbjct: 259 ADAAARFDARLMEAGVR-------VAGGTSLFRLIDDPQSAGLYKELGLAGVLVR 306


Lambda     K      H
   0.320    0.136    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: 315
Number of extensions: 17
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: 360
Length of database: 339
Length adjustment: 29
Effective length of query: 331
Effective length of database: 310
Effective search space:   102610
Effective search space used:   102610
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 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