Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate Pf1N1B4_3374 Cysteine synthase (EC 2.5.1.47)
Query= BRENDA::F4K5T2 (323 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374 Length = 324 Score = 288 bits (736), Expect = 2e-82 Identities = 162/318 (50%), Positives = 213/318 (66%), Gaps = 10/318 (3%) Query: 10 DVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLITPGK 69 D IGNTP+V +N+I V I AK+E P S+K RI +MI DAE G + PG Sbjct: 7 DNAHSIGNTPLVQINRIAPRGVT-ILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGM 65 Query: 70 STLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISIGIKG 129 T+IE T GNTGIGLA + A+RGY+++L MP++MS+ERR +L+ALGAE+ LT+ + G+KG Sbjct: 66 -TIIEPTSGNTGIGLAFVAAARGYRLVLTMPASMSIERRKVLKALGAELVLTEPAKGMKG 124 Query: 130 QLEKAKEILSKTPGGY-IPHQFINPENPEIHYRTTGPEIWRDSAGKVDILVAGVGTGGTV 188 +EKA EIL+ P Y +P QF NP NP IH +TTGPEIW D+ G VD+LVAGVGTGGT+ Sbjct: 125 AIEKAAEILASDPSTYFMPGQFENPANPAIHEKTTGPEIWSDTDGAVDVLVAGVGTGGTI 184 Query: 189 TGTGKFLKE-KNKDIKVCVVEPSESAVLSGG------KPGPHLIQGIGSGEIPANLDLSI 241 TG +++K + K I VEP S V++ KP PH IQGIG+G +P NLDLS+ Sbjct: 185 TGVSRYIKNTQGKPIISVAVEPVVSPVITQAMAGEEIKPSPHKIQGIGAGFVPKNLDLSM 244 Query: 242 VDEIIQVTGEEAIETTKLLAIKEGLLVGISSGASAAAALKVAKRPENVGKLIVVIFPSGG 301 VD + V+ +E+ L +EG+L GIS GA+ A A+++A+ PE GK IVVI P G Sbjct: 245 VDRVELVSDDESKAMALRLMQEEGILSGISCGAAMAVAVRLAETPEMQGKTIVVILPDSG 304 Query: 302 ERYLSTELFESVRYEAEN 319 ERYLS+ LF + E EN Sbjct: 305 ERYLSSMLFSDLFTEQEN 322 Lambda K H 0.314 0.136 0.378 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: 298 Number of extensions: 13 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: 323 Length of database: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 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: 42 (21.9 bits) S2: 48 (23.1 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