Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 5210129 Shew_2573 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= BRENDA::Q19842 (724 letters) >FitnessBrowser__PV4:5210129 Length = 677 Score = 494 bits (1272), Expect = e-144 Identities = 279/687 (40%), Positives = 421/687 (61%), Gaps = 29/687 (4%) Query: 49 FDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYL 108 F K+LIANRGEIACR+IKTA+ MGIKTVA++SD D ++ HV MADE+ +G + ++SYL Sbjct: 2 FTKLLIANRGEIACRIIKTAQVMGIKTVALYSDADKDARHVAMADESFYLGGSAPSESYL 61 Query: 109 RADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKK 168 + + IL+ + +GAQA+HPGYGFLSEN FA + E+AG F+GP++ AI MG K +K Sbjct: 62 KGELILEIAKRSGAQAIHPGYGFLSENADFARQCEQAGIAFVGPSADAIDAMGSKSAAKI 121 Query: 169 IATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGY 228 I A V ++PGY G+ +++ +K S++IG+P +IKA+ GGGGKGMR+ ++ +A E Sbjct: 122 IMEQANVPLVPGYHGDDQSDEVLLKASKEIGFPQLIKAAYGGGGKGMRIVESESEALEAI 181 Query: 229 RLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEE 288 +++EAASSFG+D++L+E+++ PRH+E+QV D GN ++L++R+CSIQRR+QKV+EE Sbjct: 182 NSARREAASSFGNDKLLIERYLRQPRHVEVQVFADTQGNCIYLSDRDCSIQRRHQKVVEE 241 Query: 289 APSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDS-----QRNFYFLEMNTRLQVE 343 AP+ + +RR MGE AV AKA+ Y AGTVEFL+D+ +FYF+EMNTRLQVE Sbjct: 242 APAPGLSDSLRRAMGEAAVAAAKAIDYVGAGTVEFLLDTHATEESNSFYFMEMNTRLQVE 301 Query: 344 HPITECITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRL 403 HP+TE +TG D+V+ L V+ G LP++QE V ++G +FE R+YAEDP F LP+ G+L Sbjct: 302 HPVTEMVTGQDLVKWQLMVASGSELPLSQEDVRIHGHSFEVRIYAEDPQNEF-LPASGKL 360 Query: 404 SRYVEPKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRG 463 + EP+ VR DSGIRE IS +YDP+I KL+ ++R +AL R+ AL++Y I G Sbjct: 361 NFLREPEQNRYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISG 420 Query: 464 VTHNIPLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSL---SPKEQDVVIAFASALNA 520 + HNI L +I + K F D +T ++ E Y + G +L + EQ+ +AFA+ + Sbjct: 421 LKHNIEFLANIAEHKAFSQADFSTDFI-ERYGDTLIGANLDGDNSHEQNGALAFAALYHL 479 Query: 521 RKLARANQFLNQNKQRS----THVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSAN 576 + N Q V+ F + L + + E +H + + Sbjct: 480 CAQKEQAKLTATNSQDPYSPWGQVSGFRLNRSGMHQLSLLDDEHEVQHLT----LSQIGD 535 Query: 577 KAQVRIGGKTVTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLP 636 + + + +T+SG+ L + E++G H + V + + T+ + + L Sbjct: 536 CYYLNLNDQQLTLSGE--LKQDLLHAEING-HKSKIPVSREGDDFTLFLPSGSYHFRALQ 592 Query: 637 EQAVKYLQYMKEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLH 696 + V+ ++K K +PM G I V+ GD V GQ L+VMEAMKM+ ++ Sbjct: 593 TEVVEEQANSEDKLK--------APMNGTIVTHLVEVGDEVEAGQGLMVMEAMKMEYTIE 644 Query: 697 AGKTGRVKAVNVKVGATVDEGEVLVEL 723 A G V A + G V +G +L+E+ Sbjct: 645 APFDGTVAAFFFQPGELVSDGALLLEV 671 Lambda K H 0.316 0.133 0.378 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: 1093 Number of extensions: 54 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 724 Length of database: 677 Length adjustment: 39 Effective length of query: 685 Effective length of database: 638 Effective search space: 437030 Effective search space used: 437030 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 (21.6 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