Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate CCNA_02261 CCNA_02261 propionyl-CoA carboxylase biotin-containing subunit
Query= SwissProt::Q5LUF3 (681 letters) >FitnessBrowser__Caulo:CCNA_02261 Length = 669 Score = 768 bits (1984), Expect = 0.0 Identities = 395/682 (57%), Positives = 486/682 (71%), Gaps = 16/682 (2%) Query: 1 MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60 MF+KILIANRGEIA RVIKT R++GI TV +YSDAD +L V+MADE VHIG PANQSY Sbjct: 1 MFSKILIANRGEIAVRVIKTCRRLGIKTVVVYSDADAGSLAVEMADETVHIGASPANQSY 60 Query: 61 IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120 +V DK++AA + TGAQAVHPG+GFLSEN+ FA+ EG++F+GP GAI AMGDKI SK Sbjct: 61 LVADKIIAACKQTGAQAVHPGFGFLSENAGFAQRCADEGIVFIGPNPGAISAMGDKIESK 120 Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180 K AQ A VS VPG++G I D EAVKIS +IGYPVMIKASAGGGGKG+R+AW ++ EG Sbjct: 121 KFAQAAGVSCVPGHIGEIADTAEAVKISEEIGYPVMIKASAGGGGKGIRVAWTRKDVEEG 180 Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240 F + + EA SFGDDRIFIEKF+ PRHIEIQVL D HGN ++L ERECSIQRRNQKV+E Sbjct: 181 FPAVRAEAKASFGDDRIFIEKFIESPRHIEIQVLGDKHGNVVHLFERECSIQRRNQKVIE 240 Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300 EAPSP LDEATR AMG QAVALAKAV Y SAGTVEF+ K+F+FLEMNTRLQVEHPVT Sbjct: 241 EAPSPLLDEATRNAMGAQAVALAKAVNYDSAGTVEFVAGQDKSFFFLEMNTRLQVEHPVT 300 Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360 ELITG+DLVEQMIR A GE ++ Q D+ + GWAIE+R+YAEDPYR FLPSIGRL RY P Sbjct: 301 ELITGLDLVEQMIRSAYGEKMAFGQSDLSINGWAIESRIYAEDPYRKFLPSIGRLVRYDP 360 Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420 PAE D P+G VRND GV EG EISM+YDPMI+KLCTWAPTR AAI Sbjct: 361 PAE-----------GDKDGPNGGYVVRNDAGVREGDEISMFYDPMISKLCTWAPTRLAAI 409 Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480 + M AL+ F +EG+G N+PFL+AVMD +F SG + T++I +E+P+GF G L Sbjct: 410 DGMGRALEDFHIEGLGQNIPFLAAVMDEERFRSGKLATSYIKDEFPDGFNGTTPTAVQLD 469 Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVS-F 539 + A AAM RV R + R EWVV + V + + V Sbjct: 470 ILTAVGAAMQRVYATRARSYESGLIGEAR---DEWVVAIGETRLRVKVGGEDGAVAVELL 526 Query: 540 DDGSSMRVTS-DWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPRQAE 598 D+G ++ +T DW PG + +++G ++ + GF IR R A +V V TPR AE Sbjct: 527 DEGRTLFLTDIDWRPGKPVFKAVLNGLAFTVQAAPAAEGFTIRHRAAKTRVLVLTPRSAE 586 Query: 599 LARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKG 658 L +PEK DTSK++L PMPGL+V +DV GQ+V+EG+ +C +EAMKM+NI+RAE+ G Sbjct: 587 LHDKLPEKQAADTSKLVLSPMPGLVVSMDVTTGQQVREGEVVCVLEAMKMQNIIRAERDG 646 Query: 659 VVAKINASAGNSLAVDDVIMEF 680 VV +NA G+ +A D+V++EF Sbjct: 647 VVKAVNAKGGDPVAADEVLVEF 668 Lambda K H 0.317 0.134 0.387 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: 1175 Number of extensions: 48 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: 669 Length adjustment: 39 Effective length of query: 642 Effective length of database: 630 Effective search space: 404460 Effective search space used: 404460 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