Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011781245.1 MVAN_RS20500 ATP-grasp domain-containing protein
Query= reanno::Dino:3607308 (681 letters) >NCBI__GCF_000015305.1:WP_011781245.1 Length = 660 Score = 496 bits (1277), Expect = e-144 Identities = 298/696 (42%), Positives = 400/696 (57%), Gaps = 66/696 (9%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60 MF +L+ANRGEIA RVI+T R MGI++VA++SDAD A HV AD AV IGP+PA QSY Sbjct: 1 MFGTVLVANRGEIAVRVIRTLRAMGIRSVAVFSDADAGARHVAEADVAVRIGPAPARQSY 60 Query: 61 IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120 + ++ ++ A+R+TGA+AVHPGYGFLSEN FAEAL+ G+AFIGPP AI+ MGDKI++K Sbjct: 61 LSVEALLAAVRRTGAQAVHPGYGFLSENAQFAEALDAAGIAFIGPPVAAIQTMGDKISAK 120 Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180 E V VPG + + + ++G+PV++K SAGGGGKGMR+ + +E R Sbjct: 121 AAVSEFGVPVVPGISRPGLTDQDLIAGAADVGFPVLVKPSAGGGGKGMRVVQDASELRAA 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240 S++ EAA++FGDD +F+E+FV PRHIE+QVLAD HGN ++LGERECS+QRR+QKV+E Sbjct: 181 LVSARREAASAFGDDTLFLERFVLNPRHIEVQVLADAHGNVVHLGERECSLQRRHQKVIE 240 Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR--NFYFLEMNTRLQVEHP 298 EAPSP LD TR +G +C A++V Y AGTVEFIV DR F+F+EMNTRLQVEHP Sbjct: 241 EAPSPLLDPQTRARIGAAACDTARSVDYTGAGTVEFIVSADRPDEFFFMEMNTRLQVEHP 300 Query: 299 VTELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRY 358 VTE++TG+DLVE +R+AAGEKLP+ QDD+ L G A+E R+YAEDP R FLP+ G + Sbjct: 301 VTEMVTGLDLVELQVRIAAGEKLPIAQDDIRLDGHAVEARVYAEDPARGFLPTGGDVLAL 360 Query: 359 RPPVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPA 418 R P AG VR D+G+ G + YDPM+AK+ DRP Sbjct: 361 REP----AG----------------AGVRVDSGLTRGTAVGSDYDPMLAKVIVHAGDRPT 400 Query: 419 AIEAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAAD 478 A+ A+ AL V G+ N+ F+ ++ P G + T + + PD A D Sbjct: 401 ALRALDAALADTAVLGLTTNVEFLRFLLADPDVAAGNLDTGLLDRRLPD---FAPAPATD 457 Query: 479 LTRLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTVR 538 +AAAA R R + V + W + G + Sbjct: 458 DELIAAAA--------YRWLRSWPVAPSSPWEVPSGWRIA--------------GRAATP 495 Query: 539 FADGTAHRVTSRW---TPGDSLATVEIDGAPMVLKVDKI-------TSGFRMRF--RGAD 586 F R W TPGD+ ATVE G L+ + G R + GA Sbjct: 496 FRLHAGERTDHVWLTGTPGDATATVE-GGRTRTLRASLVADRLAVTVDGMRAEYLVAGAG 554 Query: 587 VKVHVRTP-RQAELNDLMPEKLPPDTSKM----LLCPMPGLVVKIDVEVGDEVQEGQALC 641 +V + P R + ++ + PD + L PMPG VV + V+ G V G + Sbjct: 555 GQVWLAGPDRVTMVEEVREAPVRPDDAHSGDAELTSPMPGAVVAVGVDDGATVTAGTVVV 614 Query: 642 TVEAMKMENILRAEKTATVTKINAGAGDSLAVDDVI 677 TVEAMKME+ L A V ++ AG+ + V V+ Sbjct: 615 TVEAMKMEHALAAPVDG-VVELLVSAGEQVKVGQVL 649 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: 1198 Number of extensions: 51 Number of successful extensions: 6 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: 660 Length adjustment: 39 Effective length of query: 642 Effective length of database: 621 Effective search space: 398682 Effective search space used: 398682 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 24 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