Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 5210129 Shew_2573 carbamoyl-phosphate synthase L chain, ATP-binding (RefSeq)
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__PV4:5210129 Length = 677 Score = 955 bits (2468), Expect = 0.0 Identities = 485/677 (71%), Positives = 558/677 (82%), Gaps = 12/677 (1%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF KLLIANRGEIACR+I+TA+ MGIKTVA+YSDAD+DARHVA+ADESFYLG SAP+ SY Sbjct: 1 MFTKLLIANRGEIACRIIKTAQVMGIKTVALYSDADKDARHVAMADESFYLGGSAPSESY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L+GELI++IAK+ GA+AIHPGYGFLSENA FAR CE +GIAFVGP +DAIDAMGSKSAAK Sbjct: 61 LKGELILEIAKRSGAQAIHPGYGFLSENADFARQCEQAGIAFVGPSADAIDAMGSKSAAK 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 +IME+A VPLVPGYHGDDQSD LL +K+IG+P LIKAAYGGGGKGMRIVESESE A Sbjct: 121 IIMEQANVPLVPGYHGDDQSDEVLLKASKEIGFPQLIKAAYGGGGKGMRIVESESEALEA 180 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 I+SARREAASSFGNDKLL+ERYLRQPRHVEVQVFAD+QGNC+YLSDRDCSIQRRHQKVVE Sbjct: 181 INSARREAASSFGNDKLLIERYLRQPRHVEVQVFADTQGNCIYLSDRDCSIQRRHQKVVE 240 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDV-----DMSFFFMEMNTRLQV 295 EAPAPGL DSLR+ MGEAAVAAAKAIDY GAGTVEFLLD SF+FMEMNTRLQV Sbjct: 241 EAPAPGLSDSLRRAMGEAAVAAAKAIDYVGAGTVEFLLDTHATEESNSFYFMEMNTRLQV 300 Query: 296 EHPVTEMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKL 355 EHPVTEMVTGQDLVKWQL+VA+G++LPL Q +++IHGH+FEVRIYAEDP NEFLPASGKL Sbjct: 301 EHPVTEMVTGQDLVKWQLMVASGSELPLSQEDVRIHGHSFEVRIYAEDPQNEFLPASGKL 360 Query: 356 TFLREPEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGG 415 FLREPE +R+VRIDSG+RENDVISN+YDPMIAKLIVWDESRPRAL RL AL Y++ G Sbjct: 361 NFLREPEQNRYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISG 420 Query: 416 LKHNIEFLSNIAEHPAFAQANFSTDFIGRYGDALI-----GDSRDEADTAFVLAVLTQLR 470 LKHNIEFL+NIAEH AF+QA+FSTDFI RYGD LI GD+ E + A A L L Sbjct: 421 LKHNIEFLANIAEHKAFSQADFSTDFIERYGDTLIGANLDGDNSHEQNGALAFAALYHLC 480 Query: 471 LREAVSQDVA--GHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLC 528 ++ ++ A DP+SPW + GFRL+ H ++LLDD H+ + L++ Y L Sbjct: 481 AQKEQAKLTATNSQDPYSPWGQVSGFRLNRSGMHQLSLLDDEHEVQHLTLSQIGDCYYLN 540 Query: 529 LNDKLIELSGSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQVLEETA 588 LND+ + LSG ++ L EINGHK K+ VS E T+FL SGSYHFR + +V+EE A Sbjct: 541 LNDQQLTLSGELKQDLLHAEINGHKSKIPVSREGDDFTLFLPSGSYHFRALQTEVVEEQA 600 Query: 589 SSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFFAPGE 648 +SEDKLKAPMNGT+VTHLV GD+V AGQGL+VMEAMKMEYTIEAPFDG V+ FFF PGE Sbjct: 601 NSEDKLKAPMNGTIVTHLVEVGDEVEAGQGLMVMEAMKMEYTIEAPFDGTVAAFFFQPGE 660 Query: 649 LVSDGTLLLALEMADAA 665 LVSDG LLL + + A Sbjct: 661 LVSDGALLLEVTAKEDA 677 Lambda K H 0.317 0.134 0.380 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: 1287 Number of extensions: 41 Number of successful extensions: 4 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: 673 Length of database: 677 Length adjustment: 39 Effective length of query: 634 Effective length of database: 638 Effective search space: 404492 Effective search space used: 404492 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