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 Pf6N2E2_2411 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= metacyc::MONOMER-13597 (509 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2411 Length = 656 Score = 356 bits (913), Expect = e-102 Identities = 191/448 (42%), Positives = 272/448 (60%), Gaps = 3/448 (0%) Query: 1 MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60 MP FS++L+ANRGEIA R+ + + +G +AV+SEAD A+H + ADEA IG A A Sbjct: 1 MPAFSKILIANRGEIACRIQRTAQALGYRTVAVFSEADADALHVRMADEAVLIGPAAAQQ 60 Query: 61 SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120 SYLN I+DAA + DAIHPGYGFLSENA FA+A E A I FIGPS E + + K Sbjct: 61 SYLNPSAILDAARRCGADAIHPGYGFLSENAGFAKACEAADIVFIGPSPEAIDLMGSKRR 120 Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180 K AGVP G G D + A +IGYP+M+KA++GGGG G+ V + L+ Sbjct: 121 AKIAMIEAGVPCIAGYQGAAQDDDTLQREAGRIGYPLMIKASAGGGGRGMRLVQRAEDLL 180 Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240 + + A FG +L +E+ ++PRH+E Q+ GD +G + ER+C+IQRR+QK+ Sbjct: 181 EQLRGARSEALHGFGSDELILEQALIDPRHVEVQIFGDHHGQLIHLGERDCSIQRRHQKV 240 Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300 IEEAP P + + R +M + +K + +NY GT E + R FYFLE+N RLQVEH Sbjct: 241 IEEAPCPVMTTDLRRAMGDAALKAARAVNYVGAGTVEFLLAADGR-FYFLEMNTRLQVEH 299 Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360 P TELI +DLV Q+ +AAG LP QE + + G A++ R+ AED +F +G + Sbjct: 300 PVTELITGLDLVAWQLDVAAGRSLPLRQEQVT--LSGHAMQVRLYAEDPAADFLPQTGRL 357 Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420 + P+ GVR+D G+ G + P+YDS++ KLIV+G +RE A + +RA+ D + G+ Sbjct: 358 IGWEPPSQDGVRIDHGLLEGQAITPFYDSMLGKLIVHGATREEARRKLLRAVEDCVLLGV 417 Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQ 448 ++ L ++ P F +G F +I Q Sbjct: 418 QSNQRLLTGLLAHPRFIDGDFGNGFIGQ 445 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: 709 Number of extensions: 28 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: 656 Length adjustment: 36 Effective length of query: 473 Effective length of database: 620 Effective search space: 293260 Effective search space used: 293260 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