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 351443 BT1915 pyruvate carboxylase subunit A (NCBI ptt file)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__Btheta:351443 Length = 503 Score = 417 bits (1073), Expect = e-121 Identities = 224/500 (44%), Positives = 316/500 (63%), Gaps = 13/500 (2%) Query: 6 RVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYLNI 65 ++LVANRGEIA RV+++ +EM +T+IA++SEAD+ A H YADEAY +G A + +SYLNI Sbjct: 4 KILVANRGEIAIRVMRSCREMEITSIAIFSEADRTAKHVLYADEAYCVGPAASKESYLNI 63 Query: 66 EHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKRLA 125 E II+ A++ H DAIHPGYGFLSENA FA ++ I FIGP E M + DK+ + Sbjct: 64 EKIIEVAKECHADAIHPGYGFLSENATFARRCQEENIIFIGPDPETMEAMGDKISARIKM 123 Query: 126 NMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVWER 185 AGVP PG+ + S++EA++L KIGYP+M+KA+ GGGG G+ + + +++ + + Sbjct: 124 IEAGVPVVPGTQENLKSVEEAVELCNKIGYPVMLKASMGGGGKGMRLIHSAEEVEEAYTT 183 Query: 186 NKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEEAP 245 K + +FG +++EK+ P HIEFQ++GDK+GN + EREC++QRRNQK++EE P Sbjct: 184 AKSESLSSFGDDTVYLEKFVEEPHHIEFQILGDKHGNVIHLCERECSVQRRNQKIVEETP 243 Query: 246 SPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTTEL 305 S + E R+ M E + K +NY GT E D R++YFLE+N RLQVEHP TE Sbjct: 244 SVFVTPELRKDMGEKAVAAAKAVNYIGAGTIE-FLVDKHRNYYFLEMNTRLQVEHPITEE 302 Query: 306 IFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYYRE 365 + +DLVK QIK+A G+ L Q+D+ + RG AIE RI AED NF S G + E Sbjct: 303 VVGVDLVKEQIKVADGQVLQLKQKDIQQ--RGHAIECRICAEDTEMNFMPSPGIIKQITE 360 Query: 366 PTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKTTIE 425 P G GVR+DS + G +P YYD ++ KLIV+ +REYAI+ R L +YK+ G+K I Sbjct: 361 PNGIGVRIDSYVYEGYEIPIYYDPMIGKLIVWATNREYAIERMRRVLHEYKLTGVKNNIS 420 Query: 426 LYKWIMQDPDFQEGKFSTSYISQKTD---QFVKYLREQEEIKAAIAAEIQSRGLL---RT 479 + IM PDF EG + T +I++ + Q + E+ E A IAA + L R Sbjct: 421 YLRAIMDTPDFVEGHYDTGFITKNGEHLQQCIMRTSERAENIAMIAAYMDYLMNLEENRG 480 Query: 480 SSTDNKGKAQSKSGWKTYGI 499 +TDN+ S WK +G+ Sbjct: 481 DATDNR----PISKWKEFGL 496 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: 637 Number of extensions: 27 Number of successful extensions: 3 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: 503 Length adjustment: 34 Effective length of query: 475 Effective length of database: 469 Effective search space: 222775 Effective search space used: 222775 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