Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate 201056 SO1894 acetyl-CoA carboxylase, biotin carboxylase, putative (NCBI ptt file)
Query= reanno::SB2B:6937189 (673 letters) >FitnessBrowser__MR1:201056 Length = 694 Score = 962 bits (2486), Expect = 0.0 Identities = 494/676 (73%), Positives = 556/676 (82%), Gaps = 16/676 (2%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF KLLIANRGEIACR+I+TA+ MG++TVA+YSDAD++ARHVA+ADESFYLG SAPA SY Sbjct: 11 MFTKLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSY 70 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L+G+LII IAKK A+AIHPGYGFLSENA FAR CEA+GI FVGPGSDAIDAMGSKSAAK Sbjct: 71 LKGDLIIAIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAK 130 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 IM A VPLVPGYHGDDQ+DATL AEA KIG+P+LIKAAYGGGGKGMRIVE E E+ A Sbjct: 131 AIMTAAQVPLVPGYHGDDQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDA 190 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 I+SARREAASSFGNDKLLMERYLRQPRHVEVQVFAD+ GN +YLSDRDCSIQRRHQKVVE Sbjct: 191 INSARREAASSFGNDKLLMERYLRQPRHVEVQVFADTFGNAIYLSDRDCSIQRRHQKVVE 250 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 EAPAPGL D LR QMGEAAVAAAKAIDY GAGT+EFLLD D SF+FMEMNTRLQVEHPVT Sbjct: 251 EAPAPGLSDELRAQMGEAAVAAAKAIDYVGAGTIEFLLDTDNSFYFMEMNTRLQVEHPVT 310 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 EMVTGQDLVKWQL+VA+G LPL+Q E++IHGHAFEVRIYAEDP NEFLPASGKL FLRE Sbjct: 311 EMVTGQDLVKWQLMVASGQPLPLKQDEVRIHGHAFEVRIYAEDPQNEFLPASGKLNFLRE 370 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 PE S++VRIDSG+RENDVISN+YDPMIAKLIVWDESRPRAL RL AL Y++ GLKHNI Sbjct: 371 PEQSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKHNI 430 Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALIGDSRDEADTAFVLAVLTQLRLRE--AVSQD 478 EFL+NIAEHPAFA+A+FSTDFI RYGDALIG + EADTA A L Q+ R+ A +Q Sbjct: 431 EFLANIAEHPAFAKADFSTDFINRYGDALIGSASSEADTALAFAALYQVLARKEAAKAQA 490 Query: 479 VAGHDPFSPWSSLKGFRLSSPRRHSVTLLDDAHQSRSAELTESNGRYQLCLN-------- 530 + DP SPW + GFRL+S +HS+ LLDDAH+ + L + YQL N Sbjct: 491 INSADPDSPWGQVSGFRLNSVSQHSIALLDDAHELQQLVLLDFGDHYQLSHNRSSQHQLS 550 Query: 531 ----DKLI--ELSGSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQVL 584 D + LSG ++ L EINGHK KV VS + T+FL SGSYHFR V QV+ Sbjct: 551 QSAADGQVSKSLSGELKQDLLLAEINGHKSKVPVSAQGDDFTLFLPSGSYHFRAVKTQVV 610 Query: 585 EETASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEFFF 644 E +S+EDKLKAPMNGTVVTHLV G +V AGQGLLVMEAMKMEYTIEAPFDG+V+EF+F Sbjct: 611 EAESSNEDKLKAPMNGTVVTHLVDVGAEVKAGQGLLVMEAMKMEYTIEAPFDGIVTEFYF 670 Query: 645 APGELVSDGTLLLALE 660 GELVSDG +LL +E Sbjct: 671 KAGELVSDGAVLLHVE 686 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: 1289 Number of extensions: 49 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: 694 Length adjustment: 39 Effective length of query: 634 Effective length of database: 655 Effective search space: 415270 Effective search space used: 415270 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