Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate GFF1047 Psest_1080 Acetyl/propionyl-CoA carboxylase, alpha subunit
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__psRCH2:GFF1047 Length = 633 Score = 364 bits (934), Expect = e-105 Identities = 198/465 (42%), Positives = 283/465 (60%), Gaps = 4/465 (0%) Query: 7 VLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNIE 66 +LVANRGEIA RV++ K MG+T +AV+S D A H + AD +G A DSYL I+ Sbjct: 5 LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDATARHAREADIRIDLGGAKPADSYLRID 64 Query: 67 HIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLAN 126 +IDAA+ + AIHPGYGFLSENAEFA A+E+AG+ F+GP + + + K K L Sbjct: 65 KLIDAAKASGAQAIHPGYGFLSENAEFARAIEQAGLIFLGPPASAIDAMGSKSAAKALME 124 Query: 127 MAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWERN 186 AGVP PG G ++ AEKIGYP+++KA +GGGG G+ V+ + L + Sbjct: 125 EAGVPLVPGYHGEAQDVETFRAAAEKIGYPVLLKATAGGGGKGMKVVEREADLAEALASA 184 Query: 187 KRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAPS 246 +R A +FG + +EKY + PRH+E Q+ D++GN + ER+C+IQRR+QK++EEAP+ Sbjct: 185 QREAQSSFGDWRMLVEKYVLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 244 Query: 247 PALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTELI 306 P L E R +M E +K + I Y GT E D +F+F+E+N RLQVEHP TE I Sbjct: 245 PGLTPELRRAMGEAAVKAAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEHPVTEAI 303 Query: 307 FRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYREP 366 +DLV QI++A GE LP SQE + + G AIE R+ AED N+F ++G + YRE Sbjct: 304 TGLDLVAWQIRVARGEPLPISQEQV--PLIGHAIEVRLYAEDPDNDFLPATGTLDLYREA 361 Query: 367 T-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 GPG RVDSG+ G V P+YD ++ KLI +GE+RE A + L + +GG++T + Sbjct: 362 AEGPGRRVDSGVAEGDTVSPFYDPMLGKLIAWGENREEARLRLLAMLDETAVGGVRTNLA 421 Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAAE 470 + ++ F E + T++I + + ++ E + AAE Sbjct: 422 FLRRVVGHRAFAEAELDTAFIPRHESELLRPAGELSDAFWQQAAE 466 Lambda K H 0.317 0.135 0.385 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: 733 Number of extensions: 34 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: 509 Length of database: 633 Length adjustment: 36 Effective length of query: 473 Effective length of database: 597 Effective search space: 282381 Effective search space used: 282381 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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