GapMind for Amino acid biosynthesis

 

Alignments for a candidate for tyrB in Lacinutrix algicola AKS293

Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_055437263.1 ASC41_RS13945 histidinol-phosphate transaminase

Query= reanno::BFirm:BPHYT_RS14905
         (370 letters)



>NCBI__GCF_001418085.1:WP_055437263.1
          Length = 343

 Score =  155 bits (392), Expect = 2e-42
 Identities = 113/353 (32%), Positives = 180/353 (50%), Gaps = 37/353 (10%)

Query: 20  KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALS 79
           KP S    EF       V L +NENP G              +L RYPD    E+K  L+
Sbjct: 17  KPYSSARDEF--KGTADVFLDANENPFG--------------DLNRYPDPQQQEIKEKLA 60

Query: 80  ERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYA-QYSFAVYALATQGLGARAIVVP 138
               V  + + +GNGS++++++A   F E G+  V     ++ +Y ++        I  P
Sbjct: 61  ALKTVEKNQIFIGNGSDEVIDLAFRIFCEPGKDKVLTFSPTYGMYDVSANINNIEIIKQP 120

Query: 139 AVKYGHDLDAMLAAVS-----DDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVL 193
            +   +D    L  +      +D ++IF+ +PNNPTG  I    +E  L+      +V++
Sbjct: 121 LI---NDFQISLNQLQPYLDFEDIKIIFICSPNNPTGNSINPEDIEYVLENFEG--IVIV 175

Query: 194 DEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVR 253
           DEAY ++  Q     +I    +Y NL+VS+TFSKA+GLAG+RVG A A   +  L NRV+
Sbjct: 176 DEAYIDFSAQTSFIKNI---NKYNNLIVSQTFSKAWGLAGVRVGVAYANEAIIKLYNRVK 232

Query: 254 QPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGL--EYVPSDGNFVLV 311
            P+NV+TL Q A + +LN+   + ++  +  +   +L +A  KL +     P+D NF+L+
Sbjct: 233 PPYNVSTLNQEAVLKSLNNFEAVTENIQIILKERTKLKDALSKLSIVKNIHPTDANFLLI 292

Query: 312 RVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364
            V N     N+    L+++ VI+R   N  +   +RITIG  EEN+  I  L+
Sbjct: 293 EVDN----ANKTYQYLIEEKVIIRN-RNTQVDNCVRITIGTSEENDRLIKVLK 340


Lambda     K      H
   0.318    0.135    0.385 

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: 290
Number of extensions: 18
Number of successful extensions: 5
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: 370
Length of database: 343
Length adjustment: 29
Effective length of query: 341
Effective length of database: 314
Effective search space:   107074
Effective search space used:   107074
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Jul 26 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