Align Putative cystathionine gamma-lyase; EC 4.4.1.1; Gamma-cystathionase (uncharacterized)
to candidate Ga0059261_1388 Ga0059261_1388 cystathionine beta-lyase, bacterial
Query= curated2:Q59829 (392 letters) >FitnessBrowser__Korea:Ga0059261_1388 Length = 411 Score = 162 bits (410), Expect = 2e-44 Identities = 134/405 (33%), Positives = 186/405 (45%), Gaps = 38/405 (9%) Query: 11 GTGGERSASAPGDGTRAVRAGLPEPVKHEPTLPGPVFAAHFHL-----------PGDPTG 59 G G S S GDGTR V AG P + + PV+ A L D Sbjct: 12 GCGVSGSDSKKGDGTRVVGAGR-RPEWTQGIVNAPVWRASTILYDTVADLRASAGSDTHH 70 Query: 60 PYTYGRDENPTWTRLESAIGELEAPGEAGVETLVFASGMAAISSVLFSQLRAGDTAVLPD 119 YGR +PT L A+ ELE EA T ++ SG+AA+S+ L S L GD +L D Sbjct: 71 RLFYGRRGSPTQWSLAEALTELEPGAEA---TFLYPSGVAAVSAALLSVLSPGDELLLAD 127 Query: 120 DGYQAL-PLVRAQLEAYGIEVR--TAPTGRDAQLDVLDGAKLLWIETPSNPGLDVCDVRR 176 Y L+ +G+ R G + D + +++ETP + +V DV Sbjct: 128 SVYDPTRSFATGFLKRFGVITRFYDPMIGAGIAELITDKTRAIFMETPGSLTFEVQDVPA 187 Query: 177 LVEAAHAGGALVAVDNTLATPLGQRPLELGADFSVASGTKQLTGHGDVLLGYVAGRDAGA 236 +V AA A G + +DNT ATPL +E G D S+ + TK + GH DV+LG V Sbjct: 188 IVAAAKARGVVTLLDNTWATPLLFPAIEKGIDLSILACTKYVVGHSDVMLGSVT------ 241 Query: 237 MAAVRRWRKI------VGAIPGPMEAWLAHRSIATLQLRVDRQDSTALKVAEALRTRPEI 290 A W+++ +G P +AWL R + T+ LR+ + AL++A L TRPE+ Sbjct: 242 -ATAEHWQQLRATSFALGQTASPDDAWLGSRGLRTMALRLKQHGEAALEIARWLETRPEV 300 Query: 291 TGLRYPGLPDDPSHKVASQQMLRYGCVVSFTLPSRARADR--FLDALRLVEGATSFGGVR 348 + +P LP P H + + + SF L A R +D+L L S+GG Sbjct: 301 ARVLHPALPSCPGHDLFVRDFKGPAGLFSFVLRGGNEAGRAALIDSLELFGIGYSWGGFE 360 Query: 349 STA----ERRGRWGGDAVPEG-FIRLSVGAEDPDDLVADLLRALD 388 S A R R EG +RL +G EDP DL+ADL LD Sbjct: 361 SLAIPVDPDRIRTVIPWQAEGPAVRLQIGLEDPADLIADLAAGLD 405 Lambda K H 0.316 0.135 0.400 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: 452 Number of extensions: 29 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: 392 Length of database: 411 Length adjustment: 31 Effective length of query: 361 Effective length of database: 380 Effective search space: 137180 Effective search space used: 137180 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 (21.6 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