Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS32735 RR42_RS32735 3-methylcrotonyl-CoA carboxylase
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Cup4G11:RR42_RS32735 Length = 674 Score = 454 bits (1169), Expect = e-132 Identities = 276/691 (39%), Positives = 392/691 (56%), Gaps = 40/691 (5%) Query: 2 FKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYI 61 F +L+ANRGEIA R+++TAR++G+ TVA+YS+ADR+ HV AD AV IG + SY+ Sbjct: 8 FHTLLVANRGEIAMRIMRTARRLGLATVAVYSEADRHGPHVAYADRAVRIGDAAPRASYL 67 Query: 62 VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121 I +++A R++GA+AVHPGYGFL+EN FA+A+ + G+ F+GPPA AI AMG+K +K+ Sbjct: 68 NIAAIIEAARRSGADAVHPGYGFLAENAEFADAVAQAGLVFVGPPAAAIRAMGNKAEAKR 127 Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG- 180 + A++ +PGY G D ++ + IG+P+M+KA+AGGGG+GMR+ +D A G Sbjct: 128 LMLAADMPCIPGYQGEAQDDAALLQAAAPIGFPLMVKAAAGGGGRGMRLV-HDVHALPGA 186 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 S+++EA +FG ++ +E+ V PRH+EIQV ADT G+ I+LGER+CS+QRR+QKVVE Sbjct: 187 LASARSEAMAAFGSGQLILERAVIAPRHVEIQVFADTQGHVIHLGERDCSVQRRHQKVVE 246 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300 EAPSP + A R+ MG + AQA+GY AGT+EF++DGD NFYF+EMNTRLQVEH VT Sbjct: 247 EAPSPAVSPALRERMGGAAVRAAQAIGYVGAGTMEFLLDGDGNFYFMEMNTRLQVEHAVT 306 Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360 E ITG DLVE +RVAAGE LP+TQ+ V L G AIE RL AED FLP G + R+R Sbjct: 307 EAITGFDLVEWQLRVAAGEPLPVTQEQVALRGHAIEVRLTAEDVAAGFLPQGGPVLRWR- 365 Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420 AP VR D + EGGEI ++YD M+AKL T G R A Sbjct: 366 ------------------APGAGHDVRVDHALQEGGEIPVHYDSMVAKLVTHGATREEAR 407 Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480 + A++ + G+ N F+A + H F ++ T F+ AA + Sbjct: 408 RKLLRAVEQTVLLGVASNQGFLADCLAHEAFAGNQVHTGFVDTHMQAALRTTQPAAAQVA 467 Query: 481 RLAAAAAAMFRVAE---IRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPG-GST 536 A AAA + +E + S L E+ D AQ ++V + G G Sbjct: 468 CAALAAAGLLAASECPALVAPACSLGLQAGEQQWRVDLRAVAQG--WEVAVRGGEGEGEG 525 Query: 537 VRFADGTAHRVTS----RWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVR 592 DGT+ + S R A VE +G M L + T G + A R Sbjct: 526 EGEGDGTSAEIVSVRVLRADLEQGSALVECNG--MALPLVFATGGDAVHLFSAG-----R 578 Query: 593 TPRQAELNDLMPEKLPPDTSKM--LLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMEN 650 R A L+ ++ P D + LL P+ +V + G+ V GQ L +EAMKME+ Sbjct: 579 AWRFARLDPRQKKRNPGDAGRAGELLAPLTARIVAVKAAAGEAVLAGQVLVVLEAMKMEH 638 Query: 651 ILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681 + A + +++A G ++++ + Sbjct: 639 AIVAPFDGVIAQLHAREGGQARAGSLLVKVD 669 Lambda K H 0.318 0.134 0.392 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: 1136 Number of extensions: 56 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: 681 Length of database: 674 Length adjustment: 39 Effective length of query: 642 Effective length of database: 635 Effective search space: 407670 Effective search space used: 407670 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: 54 (25.4 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