Align Cystathionine beta-lyase, chloroplastic; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate BPHYT_RS13720 BPHYT_RS13720 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::P53780 (464 letters) >FitnessBrowser__BFirm:BPHYT_RS13720 Length = 450 Score = 200 bits (508), Expect = 9e-56 Identities = 137/401 (34%), Positives = 196/401 (48%), Gaps = 43/401 (10%) Query: 103 AMSTPLYQTATFKQPSA--------IENGPYDYTRSGNPTRDALESLLAKLDKADRAFCF 154 A +TP+YQT +F + +E + Y+R NPT E +A L+ A Sbjct: 23 ARATPIYQTTSFSFRDSDHAAALFNMERAGHVYSRISNPTVAVFEERVAALENGAGAIGT 82 Query: 155 TSGMAALS-AVTHLIKNGEEIVAGDDVYGGSDRLLSQVVPRSGVVVKRVNTTKLDEVAAA 213 SG AAL A+ L+ G IVA +YGGS LL + R G+ V LD AA Sbjct: 83 ASGQAALHLAIATLMGAGSHIVASSALYGGSHNLLHYTLRRFGIETTFVKPGDLDAWRAA 142 Query: 214 IGPQTKLVWLESPTNPRQQISDIRKISEMAHAQGALVLVDNSIMSPVLSRPLELGADIVM 273 + P T+L++ E+ NP + DI ++++AH +LVD++ +P L +P E GAD V Sbjct: 143 LRPNTRLLFGETLGNPGLDVLDIAAVAQIAHEHRVPLLVDSTFTTPYLLKPFEHGADFVY 202 Query: 274 HSATKFIAGHSDVMAGVLAVKG----EKLAKEVYFLQN---------SEGSGLAPF---- 316 HSATKF+ GH + GVL G E + F + SE S +APF Sbjct: 203 HSATKFLGGHGTTIGGVLVDGGTFDFEASGRFPEFTEPYDGFHGMVFSEESTVAPFLLRA 262 Query: 317 ---------------DCWLCLRGIKTMALRIEKQQENARKIAMYLSSHPRVKKVYYAGLP 361 W L+GI+T+ LR+E+ N R++ +L++H V+ V Y LP Sbjct: 263 RREGLRDFGACLHPQAAWQLLQGIETLPLRMERHVANTRRVVEFLAAHAAVESVAYPELP 322 Query: 362 DHPGHHL-HFSQAKGAGSVFSF-ITGSVALSKHLVETTKYFSIAVSFGSVKSLISMPCFM 419 HP H L +GAG+VFSF + G A + +E FS + G +SL+ P Sbjct: 323 THPDHALAKRLLPRGAGAVFSFNLRGDRAAGRSFIEALSLFSHLANVGDARSLVIHPAST 382 Query: 420 SHASIPAEVREARGLTEDLVRISAGIEDVDDLISDLDIAFK 460 +H + A A G+ E +R+S G+ED DDLI DL A K Sbjct: 383 THFRMDAAALAAAGIAEGTIRLSIGLEDPDDLIDDLKRALK 423 Lambda K H 0.316 0.130 0.369 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: 408 Number of extensions: 27 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: 464 Length of database: 450 Length adjustment: 33 Effective length of query: 431 Effective length of database: 417 Effective search space: 179727 Effective search space used: 179727 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: 51 (24.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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