Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012277981.1 SHAL_RS15030 ATP-grasp domain-containing protein
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000019185.1:WP_012277981.1 Length = 702 Score = 487 bits (1253), Expect = e-142 Identities = 281/686 (40%), Positives = 406/686 (59%), Gaps = 45/686 (6%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60 MF K+LIANRGEIACR+I TA+ MG++TVA+YSDAD +A HV+MADEA ++G SY Sbjct: 1 MFTKLLIANRGEIACRIINTAKVMGVRTVALYSDADIDARHVAMADEAFYLGGSAPADSY 60 Query: 61 IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120 + + I+E K +GAEA+HPGYGFLSE DFA E A + F+GP + AI++MG K +K Sbjct: 61 LKGELIIEIAKRAGAEAIHPGYGFLSENADFALKCEQANIAFVGPSAAAIDSMGSKSAAK 120 Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180 ++ A V VPGY G + + V +N++G+P++IKA+ GGGGKGMRI S EV + Sbjct: 121 EIMGAANVPLVPGYHGDAQNDELLVSEANKMGFPLLIKAAFGGGGKGMRIVESNNEVLDA 180 Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240 S++ EA +SFG+D++ +E+++ QPRH+E+QV AD HGNC+YL +R+CSIQRR+QKV+E Sbjct: 181 IHSARREAISSFGNDKLLMERYLRQPRHVEVQVFADSHGNCIYLSDRDCSIQRRHQKVVE 240 Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAP+P L +A R MGE A A AKA+ Y AGTVEF++D +FYF+EMNTRLQVEHPVT Sbjct: 241 EAPAPGLSDALRVKMGEAAVAAAKAINYEGAGTVEFLLDTDDSFYFMEMNTRLQVEHPVT 300 Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360 EL+TG DLV+ + VA+G LP +Q++++I G A E+R+YAEDP+ +FLP+ G+L R Sbjct: 301 ELVTGQDLVKWQLMVASGSPLPLKQNEVRIVGHAFEARIYAEDPHNDFLPASGKLDFLRE 360 Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420 P +S VR D+GV E IS +YDPMI+KL TW +R A++ + ALD +++ G+ Sbjct: 361 PEQS----QFVRIDSGVRENDVISNFYDPMISKLITWDESRPRALQRLVHALDDYQISGL 416 Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLD-EPTLRR-VAAAAAAMNRVA 478 HN+ F+ + H F + +T FI E Y D A + P+ RR A A AA+ ++ Sbjct: 417 KHNIEFLANIAKHQAFSDANFSTDFI-ERYGDALLTAQSNATPSTRRDTALAIAALYQLC 475 Query: 479 EIRRTRISGTMNNHERHVGVDWVVALQ---GESYHVSIAADREGSTVSFSDGSSLRVTSD 535 ++ + T+ +H+ + V + + V++ D + + L + Sbjct: 476 ARKKQAKNDTLTSHDPYSPWGKVSGFRLNSASQHQVALLDDNH-------EINHLELIET 528 Query: 536 WTPGQPLASLMVDGRPLVM----------------KVGKIPM-------GFRLRLR---- 568 G+P L + L + K+G G +++L Sbjct: 529 QVAGKPQYQLQLSDNLLTLSGELIDEILHAEIVQHKLGDSQAEQASKANGHKIKLPVSQV 588 Query: 569 GADLKVNVRTPRQAELALLMPEKLPPDT-SKYLLCPMPGLVVKINVAEGDEVQEGQALAT 627 G D + + + AL E D L PM G +V V+ GD V+ GQ + Sbjct: 589 GNDFTLFINSKSYHYRALESEEIEEQDNLEDKLKAPMNGTIVTQLVSVGDVVKAGQGIMV 648 Query: 628 VEAMKMENILRAERRGTVKKIAAAPG 653 +EAMKME + + G V PG Sbjct: 649 MEAMKMEYTIESPFDGVVSAFFFEPG 674 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: 1018 Number of extensions: 39 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 666 Length of database: 702 Length adjustment: 39 Effective length of query: 627 Effective length of database: 663 Effective search space: 415701 Effective search space used: 415701 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