Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate 207710 DVU2226 acetyl-CoA carboxylase, biotin carboxylase, putative
Query= reanno::pseudo1_N1B4:Pf1N1B4_3984 (651 letters) >MicrobesOnline__882:207710 Length = 471 Score = 219 bits (559), Expect = 2e-61 Identities = 164/463 (35%), Positives = 240/463 (51%), Gaps = 51/463 (11%) Query: 9 LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKA---ADSYL 65 +LVANRGEIA R++R LGL V++A D + H R A +LGG+ + SY Sbjct: 8 VLVANRGEIATRIVRACHRLGLEFTCVYTAEDAASGHVRLAR---ELGGANSLYRVSSYH 64 Query: 66 QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAI--EAAGLIFLGPPASAIDAMGSKSAA 123 ++L+A A +G A+HPGYGF +E+ FAR + LIF+GP I +G K Sbjct: 65 DANELLAVADDAGCTAVHPGYGFFAEDYRFARRVAQRERKLIFIGPSWRVIRELGDKINT 124 Query: 124 KALMETAGVPLVPGYHGE----------AQDLETFRDACERIGYP-VLLKATAGGGGKGM 172 K L + GVP VPG AQ L F++ + I P VL+KA+AGGGG G+ Sbjct: 125 KRLARSLGVPTVPGSDKPIYDELEAEKVAQSLYEFQEQ-QGIRRPLVLVKASAGGGGMGI 183 Query: 173 KVVEDVSQLAEALASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHG-NCLYLNER 231 + V D+ + AL F D +L+E+ + H+E+Q+ +D+ G N ++ R Sbjct: 184 EEVYDLDLFKSVYRRIRNYALRQFKDEGVLIEQRIRDFNHLEVQIVSDRTGRNPVHFGTR 243 Query: 232 DCSIQR-RHQKVVEEAPAPGLSP----------ELRRAMGEAAVRSAQAIGYVGAGTVEF 280 +CSIQ QK +E APG P ++ R + ++ A+ +GY GT E+ Sbjct: 244 NCSIQSIGLQKRIE--VAPGFDPTSIEYGFDAAQVLRDITYHSLAMARKVGYDNVGTWEW 301 Query: 281 LLDARGEFFFMEMNTRLQVEHPVTEAIT-----GLDLVAWQIRVARGEALPMTQDQVPLI 335 ++ G F ME+NTR+QVE+ V+ I +DL+A QIR+ G+ L Q+ + Sbjct: 302 IVTRDGHPFLMEVNTRIQVENGVSARIARVNGQEVDLIAEQIRIGLGQPLGYGQEDITFE 361 Query: 336 GHAIEVRLYAEDPGNDFLPATGRLALY---RESAAGPGRRVDSGVEEGDEISPFYDPMLG 392 G IE RL AEDP N F P GR+ + E A V + EE +I +DP L Sbjct: 362 GVGIEYRLIAEDPDNRFTPWVGRIDAFGWPEEDWARMYTHVPT--EEPYDIPTEFDPNLA 419 Query: 393 KLIAWGEDREQARLRLLSMLDEFAIGG-------LKTNINFLR 428 I WG+D E+ + R +S L+ + G L++N+NFLR Sbjct: 420 LAIIWGKDLEEVKRRGVSFLEGLTLQGQNKAGDELRSNVNFLR 462 Lambda K H 0.318 0.134 0.386 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: 638 Number of extensions: 35 Number of successful extensions: 7 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: 651 Length of database: 471 Length adjustment: 36 Effective length of query: 615 Effective length of database: 435 Effective search space: 267525 Effective search space used: 267525 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 (21.7 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