Align Putative cysteine synthase; EC 2.5.1.47; O-acetylserine (Thiol)-lyase; O-acetylserine sulfhydrylase; CSase (uncharacterized)
to candidate AO356_28790 AO356_28790 cysteine synthase
Query= curated2:P55708 (336 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28790 Length = 347 Score = 474 bits (1221), Expect = e-138 Identities = 232/329 (70%), Positives = 275/329 (83%) Query: 1 MLHTTVTQLIGQTPVMSIDVPGRNATLVLKIEKNNPGGSMKDRMARSMVIAALQDGRLPP 60 M+ V+ LIG TP++ ID+P +A L+LKIEKNNPGGS+KDRMAR+MV+AAL+ GRL P Sbjct: 1 MILNKVSDLIGNTPMLGIDIPDTHARLLLKIEKNNPGGSIKDRMARNMVLAALKSGRLKP 60 Query: 61 GGTIVESSSGNTGTGLALAALEFGLRFIAVVDHHAAPDKIRMMRALGAEIRYVEGDFRED 120 GG +VESSSGNTG GLA+AA+EFGL FIAVVDHHAA DKI +M+ALGA++R+V G +RED Sbjct: 61 GGVVVESSSGNTGIGLAMAAVEFGLHFIAVVDHHAAQDKIAVMKALGADVRFVAGHYRED 120 Query: 121 EVAVVERQRLAAQLGAQLPGALFMNQSDNPANPEGYTGLVDELVAQLPDGIDAFVGCVGT 180 EVAVVERQR+AA+L Q+PGA+FMNQSDN AN GY+ V E +AQ+ + A+VGCVGT Sbjct: 121 EVAVVERQRMAAELAQQIPGAVFMNQSDNAANAGGYSDFVRETIAQVEGKVGAYVGCVGT 180 Query: 181 GGSMTGISQRLKRNNPAVRTIAVEPAGSIVFGKPGHPYYQSGTGTPAGDEVGKVLDYGCI 240 GGSMTGI++ LK +NP T+AVEPAGSIVFG PG+PYYQSGTGTPAGD VG VLDY CI Sbjct: 181 GGSMTGIARGLKLHNPDTVTVAVEPAGSIVFGHPGYPYYQSGTGTPAGDTVGLVLDYSCI 240 Query: 241 DEGVQVTDTQAFETARYIARRKGLLVGGSTGGAIYKALEFIGAGKLTGTVVTTVADGGEK 300 D GVQVTD+QAFETARYIAR GLLVGGSTGGAI+KALEFI G LTG VV +ADGGEK Sbjct: 241 DLGVQVTDSQAFETARYIARNLGLLVGGSTGGAIFKALEFIHKGVLTGNVVVPIADGGEK 300 Query: 301 YLGTIFDEEWMAKRRLLDPAIAAQLDGWL 329 YL T+FD++W+ +R LLDP +A QLDGWL Sbjct: 301 YLHTVFDDQWLQERDLLDPGVAVQLDGWL 329 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: 542 Number of extensions: 20 Number of successful extensions: 1 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: 347 Length adjustment: 29 Effective length of query: 307 Effective length of database: 318 Effective search space: 97626 Effective search space used: 97626 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