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 GFF4012 Psest_4085 Biotin carboxylase
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__psRCH2:GFF4012 Length = 471 Score = 419 bits (1077), Expect = e-121 Identities = 218/467 (46%), Positives = 315/467 (67%), Gaps = 6/467 (1%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++L+ANRGEIA R+++A EMG+ ++AV+SEAD++A+H K ADEA++IG+ P L YLN Sbjct: 4 KLLIANRGEIAVRIVRACAEMGVRSVAVFSEADRHALHVKRADEAHFIGEDP-LAGYLNP 62 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 +++ A + DA+HPGYGFLSENAE A+ + GI F+GPS+EV+R++ DK + +R Sbjct: 63 RKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFVGPSAEVIRRMGDKTEARRSM 122 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 AGVP PG++G V + EAL+ AE+IGYP+M+KA SGGGG GI R ++Q +L + R Sbjct: 123 IKAGVPVTPGTEGNVRDLAEALREAERIGYPVMLKATSGGGGRGIRRCNSQAELESAYPR 182 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 A +AFG A++F+EK V P+HIE Q++ D +GN V +ER+C+IQRRNQKLIE AP Sbjct: 183 VISEATKAFGSAEVFLEKCIVEPKHIEAQILADSFGNTVHLFERDCSIQRRNQKLIEIAP 242 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 SP L E+R + + ++ K + Y GT E +D + YF+E+N R+QVEH TE Sbjct: 243 SPQLTPEQRAYIGDLAVRAAKAVGYENAGTVEFLLAD--GEVYFMEMNTRVQVEHTITEE 300 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 I ID+V+ QI++A+G+ L QED+ RG ++++RINAED NNF G +T Y Sbjct: 301 ITGIDIVREQIRIASGQPLSVKQEDIQH--RGFSLQFRINAEDPRNNFLPCFGKITRYYA 358 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 P GPGVR D+ I +G +PPYYDS+ KL+V+ + E A+ G RAL D ++ G+KTT Sbjct: 359 PGGPGVRTDTAIYTGYTIPPYYDSMCLKLVVWALTWEEALARGSRALDDMRVQGVKTTAT 418 Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTDQF-VKYLREQEEIKAAIAAEI 471 Y+ I+ +PDF+ G+F+TS++ + R+ E+ AIAA I Sbjct: 419 YYQQILANPDFRSGQFNTSFVDNHPELLNYSIKRKPGELALAIAAAI 465 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: 572 Number of extensions: 21 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: 471 Length adjustment: 34 Effective length of query: 475 Effective length of database: 437 Effective search space: 207575 Effective search space used: 207575 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: 52 (24.6 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