Align Putative cysteine synthase; EC 2.5.1.47; O-acetylserine (Thiol)-lyase; O-acetylserine sulfhydrylase; CSase (uncharacterized)
to candidate 3609567 Dshi_2951 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= curated2:P55708 (336 letters) >FitnessBrowser__Dino:3609567 Length = 380 Score = 122 bits (305), Expect = 2e-32 Identities = 99/339 (29%), Positives = 158/339 (46%), Gaps = 37/339 (10%) Query: 8 QLIGQTPVMSIDVPG-RNATLVLKIEKNNPGGSMKDRMARSMVIAALQDGRLPPGGTIVE 66 Q T + +++PG R L LK E +P GS+K R+ARS+ + AL +G+L G ++E Sbjct: 47 QRSADTHLFKLELPGLRGVDLYLKDESTHPTGSLKHRLARSLFLYALCNGQLCAGRPVIE 106 Query: 67 SSSGNTGTGLALAALEFGLRFIAVVDHHAAPDKIRMMRALGAEIRYVEGDFREDEVAVVE 126 +SSG+T A A GL FIAV+ A KI + G +V+ + E Sbjct: 107 ASSGSTAVSEAYFAQMLGLPFIAVMPRRTARSKIAEITRFGGTCHFVD--------SAPE 158 Query: 127 RQRLAAQLGAQLPGALFMNQ---SDNPANPEGYTGLVDELVAQLPDG----IDAFVGCVG 179 A L A+ G FM+Q ++ + G + + + Q+ A V G Sbjct: 159 MHAAATTLAAE-TGGYFMDQFLYAERATDWRGNNNIAESIFRQMARERFPIPAALVMSAG 217 Query: 180 TGGSMTGISQRLKRNNPAVRTIAVEPAGSIVFGKPGHPYYQSGTGTPAGDEVGKVLDYG- 238 TGG+ + + ++ + + V+P S+ + Y SG T + ++ G Sbjct: 218 TGGTSATLGRYIRYRGFETQLVVVDPENSVFYDS-----YMSGDATLSRACSSRIEGIGR 272 Query: 239 ----------CIDEGVQVTDTQAFETARYIARRKGLLVGGSTGGAIYKALEF---IGAGK 285 ID +QV DT + TA +++ R G VGGSTG ++ AL+ + A Sbjct: 273 PIVEKSFQPDVIDTMLQVPDTASVATALWLSDRIGRKVGGSTGTNLWGALQIADRMQAAG 332 Query: 286 LTGTVVTTVADGGEKYLGTIFDEEWMAKR-RLLDPAIAA 323 G++VT + D GE+YL T D +W+A+ + PA AA Sbjct: 333 TEGSIVTVMCDAGERYLDTYHDPDWVAREIGDIGPACAA 371 Lambda K H 0.318 0.137 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: 348 Number of extensions: 21 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: 336 Length of database: 380 Length adjustment: 29 Effective length of query: 307 Effective length of database: 351 Effective search space: 107757 Effective search space used: 107757 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: 49 (23.5 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