Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate AZOBR_RS07765 AZOBR_RS07765 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::acidovorax_3H11:Ac3H11_2452 (415 letters) >FitnessBrowser__azobra:AZOBR_RS07765 Length = 429 Score = 234 bits (598), Expect = 3e-66 Identities = 153/431 (35%), Positives = 229/431 (53%), Gaps = 18/431 (4%) Query: 1 MTTPQNQSFTTQIVHADRLGGAEQGAIHQPIHTSVQYGYDKVEDLIAVFQGTAKGGFNYA 60 M+ ++ F T+ +HA GA PI+ + + +D V+D ++F K GF Y+ Sbjct: 1 MSEQKSFGFETRAIHAGAAPDPATGARQTPIYQTTSFVFDDVDDAASLFN-LQKVGFIYS 59 Query: 61 RQGTPTTAALEAKITKMERGHGTIVFSSGMAGICAVFLTLLKAGDHLVASQFVFGNTNSV 120 R PT + LE ++ +E G G SSG A L++ GD +VAS+ ++G T + Sbjct: 60 RLTNPTVSVLEERLANLEGGAGATATSSGHAAQLLALFPLMEPGDEIVASRKLYGGTLNQ 119 Query: 121 LGTLAD--LGVEVTTVDVTDAANVAAALRPNTRMVFVETIANPGTQIPDLEGIGALCKAH 178 LGT G + VD NV AA+ T+ +FVE++ANPG + DLE I + Sbjct: 120 LGTSFPRAFGWKSVFVDTDQPENVRAAITAKTKAIFVESLANPGGVVTDLEAIAKIADEA 179 Query: 179 GALYVVDNTVASPYLFRAATVGAGLVVNSLTKSIGGLGDALGGAITDTGLYDWSRYPNIF 238 G +VDNT+A+PYL GA LVV+S TK + G G ++GG + D+G +DW + F Sbjct: 180 GIPLIVDNTLATPYLINPIQWGATLVVHSTTKFLSGNGTSVGGVVIDSGSFDWGK-SGKF 238 Query: 239 AAYRKGDAKGWGLQ------------QLRKKGLRDMGGTLSSHAAHQLALGAETLALRMD 286 A + DA GL+ GLRD+G + + A G ETL LRM Sbjct: 239 PALSEPDAGYHGLKFQETFGHLAFTIHGHAVGLRDLGPSQAPLNAFLTLNGIETLPLRMQ 298 Query: 287 RTSATALALAQWLEAHPAIARVHYPLLPSHPQHAFAKKHLKAGSW-LLSFELRDP-DQCL 344 R S +AL +AQ+LE+HPA+ V Y L S +A AKK+L G+ +L+F ++ D + Sbjct: 299 RHSDSALKVAQFLESHPAVGWVSYAGLESSKYNALAKKYLPKGAGAVLTFGVKGGFDTGV 358 Query: 345 PVCNRLQLPIKATGLADTRTLIIPVAHTIFWEAGPAVRASMGIADSMIRLSVGLEEVEDL 404 V +QL + D+R+LII + T + P +A G ++RLS+GLE VED+ Sbjct: 359 KVVENVQLLSHLANIGDSRSLIIHPSSTTHRQLSPEGQAQAGAGPDVLRLSIGLESVEDI 418 Query: 405 LADFEQALAGA 415 +AD ++AL+ A Sbjct: 419 IADLDRALSAA 429 Lambda K H 0.320 0.134 0.398 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: 445 Number of extensions: 25 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: 415 Length of database: 429 Length adjustment: 32 Effective length of query: 383 Effective length of database: 397 Effective search space: 152051 Effective search space used: 152051 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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