GapMind for Amino acid biosynthesis

 

Alignments for a candidate for metY in Burkholderia phytofirmans PsJN

Align O-acetylhomoserine aminocarboxypropyltransferase (EC 2.5.1.49) (characterized)
to candidate BPHYT_RS13720 BPHYT_RS13720 O-acetylhomoserine aminocarboxypropyltransferase

Query= BRENDA::L7N4M1
         (449 letters)



>FitnessBrowser__BFirm:BPHYT_RS13720
          Length = 450

 Score =  461 bits (1186), Expect = e-134
 Identities = 234/426 (54%), Positives = 302/426 (70%), Gaps = 3/426 (0%)

Query: 18  FETKQIHAGQHPDPTTNARALPIYATTSYTFDDTAHAAALFGLEIPGNIYTRIGNPTTDV 77
           F+T  +HAG  PDPTT ARA PIY TTS++F D+ HAAALF +E  G++Y+RI NPT  V
Sbjct: 6   FDTLALHAGAAPDPTTGARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAV 65

Query: 78  VEQRIAALEGGVAALFLSSGQAAETFAILNLAGAGDHIVSSPRLYGGTYNLFHYSLAKLG 137
            E+R+AALE G  A+  +SGQAA   AI  L GAG HIV+S  LYGG++NL HY+L + G
Sbjct: 66  FEERVAALENGAGAIGTASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFG 125

Query: 138 IEVSFVDDPDDLDTWQAAVRPNTKAFFAETISNPQIDLLDTPAVSEVAHRNGVPLIVDNT 197
           IE +FV  P DLD W+AA+RPNT+  F ET+ NP +D+LD  AV+++AH + VPL+VD+T
Sbjct: 126 IETTFVK-PGDLDAWRAALRPNTRLLFGETLGNPGLDVLDIAAVAQIAHEHRVPLLVDST 184

Query: 198 IATPYLIQPLAQGADIVVHSATKYLGGHGAAIAGVIVDGGNFDW-TQGRFPGFTTPDPSY 256
             TPYL++P   GAD V HSATK+LGGHG  I GV+VDGG FD+   GRFP FT P   +
Sbjct: 185 FTTPYLLKPFEHGADFVYHSATKFLGGHGTTIGGVLVDGGTFDFEASGRFPEFTEPYDGF 244

Query: 257 HGVVFAELGPPA-FALKARVQLLRDYGSAASPFNAFLVAQGLETLSLRIERHVANAQRVA 315
           HG+VF+E    A F L+AR + LRD+G+   P  A+ + QG+ETL LR+ERHVAN +RV 
Sbjct: 245 HGMVFSEESTVAPFLLRARREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVV 304

Query: 316 EFLAARDDVLSVNYAGLPSSPWHERAKRLAPKGTGAVLSFELAGGIEAGKAFVNALKLHS 375
           EFLAA   V SV Y  LP+ P H  AKRL P+G GAV SF L G   AG++F+ AL L S
Sbjct: 305 EFLAAHAAVESVAYPELPTHPDHALAKRLLPRGAGAVFSFNLRGDRAAGRSFIEALSLFS 364

Query: 376 HVANIGDVRSLVIHPASTTHAQLSPAEQLATGVSPGLVRLAVGIEGIDDILADLELGFAA 435
           H+AN+GD RSLVIHPASTTH ++  A   A G++ G +RL++G+E  DD++ DL+    A
Sbjct: 365 HLANVGDARSLVIHPASTTHFRMDAAALAAAGIAEGTIRLSIGLEDPDDLIDDLKRALKA 424

Query: 436 ARRFSA 441
           A++ SA
Sbjct: 425 AQKASA 430


Lambda     K      H
   0.318    0.134    0.394 

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: 623
Number of extensions: 23
Number of successful extensions: 4
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: 449
Length of database: 450
Length adjustment: 33
Effective length of query: 416
Effective length of database: 417
Effective search space:   173472
Effective search space used:   173472
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: 51 (24.3 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