Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate 3607893 Dshi_1301 Carbamoyl-phosphate synthase L chain ATP-binding (RefSeq)
Query= reanno::Dino:3607308 (681 letters) >FitnessBrowser__Dino:3607893 Length = 661 Score = 443 bits (1140), Expect = e-128 Identities = 291/684 (42%), Positives = 376/684 (54%), Gaps = 70/684 (10%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF++ILIANRGEIACRVI T R++G+QTVA++SD D A HV MAD AV++G + SY Sbjct: 1 MFERILIANRGEIACRVIDTCRRLGVQTVAVHSDVDAGARHVAMADMAVNLGGAAPRDSY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + + ++ A R TGAEA+HPGYGFLSEN F EA+ G+ FIGP A AI AMG K +K Sbjct: 61 LRGEAIIAAARATGAEAIHPGYGFLSENPDFVEAVAAAGLVFIGPSAAAIRAMGLKDAAK 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 + EA V VPGY G D + IGYPV+IKA AGGGGKGMR E EG Sbjct: 121 ALMAEAGVPVVPGYQGADQDPARLAAEAEAIGYPVLIKAVAGGGGKGMR----RVEGPEG 176 Query: 181 F----QSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQ 236 F ++++ EA +FG+D + +EK+V PRHIE+QV D ++L ER+CS+QRR+Q Sbjct: 177 FAGALEAARAEARGAFGNDHVLLEKYVATPRHIELQVFGD-GARAVHLFERDCSLQRRHQ 235 Query: 237 KVVEEAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGD-----RNFYFLEMNT 291 KV+EEAP+P + R AMG + A+A+GYA AGTVEFIVD F+F+EMNT Sbjct: 236 KVIEEAPAPGMTPEMRAAMGAAAVRAAEAIGYAGAGTVEFIVDASDGLRPDRFWFMEMNT 295 Query: 292 RLQVEHPVTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPS 351 RLQVEHPVTE +TGVDLV +RVA+GE LP Q+D++L G A E RLYAED + FLP+ Sbjct: 296 RLQVEHPVTEAVTGVDLVAWQLRVASGEPLPARQEDLSLRGHAFEARLYAEDVPKGFLPA 355 Query: 352 IGRLTRYRPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCT 411 GRLT P + R +TGV G EIS +YDPMIAKL Sbjct: 356 TGRLTHLAFPAD----------------------ARIETGVRAGDEISPWYDPMIAKLVV 393 Query: 412 WGPDRPAAIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEG 471 GP R +A+ + L G EV G NL F+ A+ H F GE+ T I E Sbjct: 394 HGPTRQSALRKLDRVLAGCEVAGSVTNLAFLRALARHGGFFAGEVDTGLIDR------EV 447 Query: 472 VTLGAADLTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDW--VVTAQDARF-DVTI 528 TL A + A A A A + G T W +V AQ RF + I Sbjct: 448 ETLSPAPVPCSRARALAALGAAGLHEGGPDGA-------GFTLWAPLVQAQGLRFGEAEI 500 Query: 529 DA---DPGGSTVRFADGTA-HRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRG 584 +A G + R G A H +T R +DGAP ++ +G + F G Sbjct: 501 EARIETRGAGSFRVGIGEATHEITRRG------GAWWVDGAPTPARIVVHAAGVSV-FWG 553 Query: 585 ADVKVHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVE 644 + H P + L + + PMPGLV + V GD V +G L +E Sbjct: 554 NN--YHFTAP-----DPLHRAGAAGPGAGHVEAPMPGLVKAVFVAPGDTVAQGARLAILE 606 Query: 645 AMKMENILRAEKTATVTKINAGAG 668 AMKME+ L A + V+++ G Sbjct: 607 AMKMEHTLTAGRDGVVSEVLVAEG 630 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: 1190 Number of extensions: 60 Number of successful extensions: 5 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: 661 Length adjustment: 39 Effective length of query: 642 Effective length of database: 622 Effective search space: 399324 Effective search space used: 399324 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