Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_002720336.1 RSPH17029_RS09225 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::SB2B:6937189 (673 letters) >NCBI__GCF_000015985.1:WP_002720336.1 Length = 448 Score = 413 bits (1062), Expect = e-120 Identities = 221/451 (49%), Positives = 292/451 (64%), Gaps = 3/451 (0%) Query: 1 MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60 MF K+LIANRGEIA RVIR ++MGIK+VAV+S AD DA HV +ADES +G ++ SY Sbjct: 1 MFEKILIANRGEIALRVIRACQEMGIKSVAVHSTADADAMHVRMADESVCIGPASSTDSY 60 Query: 61 LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120 L II + GAEA+HPGYGFLSENAAFA+A + GI F+GP +D I MG K AK Sbjct: 61 LNKASIISACEITGAEAVHPGYGFLSENAAFAQALQDHGIEFIGPTADHIRIMGDKITAK 120 Query: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180 M+ GVP VPG G T +A A+ IG+P++IKA GGGG+GM++ +E EL+ A Sbjct: 121 DTMKALGVPCVPGSDGGVPDYETAIATARDIGFPVIIKATAGGGGRGMKVARNEQELEIA 180 Query: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240 +AR EA ++FGND++ ME+YL++PRH+E+QVF D +G V+L +RDCS+QRRHQKV E Sbjct: 181 FRTARSEAKAAFGNDEVYMEKYLQKPRHIEIQVFGDGKGRAVHLGERDCSLQRRHQKVFE 240 Query: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300 EAP P + +R ++G A I+Y GAGT+EFL + D F+F+EMNTRLQVEHPVT Sbjct: 241 EAPGPVITPEMRAEIGRICADAVARINYIGAGTIEFLYE-DGQFYFIEMNTRLQVEHPVT 299 Query: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360 E + G DLV+ Q+ VAAG + Q ++I+GHA EVRI AE N F P GK+ Sbjct: 300 EAIFGVDLVREQIRVAAGLPMSFNQEALEINGHAIEVRINAEKLPN-FSPCPGKVRVFHA 358 Query: 361 PEPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGLKHNI 420 P VR+DS + I YYD +I KLIV RP ALARL RALG+ V G+ + Sbjct: 359 P-GGLGVRMDSALYGGYSIPPYYDSLIGKLIVHGRDRPEALARLHRALGELIVDGIDTTV 417 Query: 421 EFLSNIAEHPAFAQANFSTDFIGRYGDALIG 451 + P +++ ++ ++ A G Sbjct: 418 PLFHALLAEPDIQNGDYNIHWLEKWLAAQFG 448 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: 741 Number of extensions: 30 Number of successful extensions: 4 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: 673 Length of database: 448 Length adjustment: 36 Effective length of query: 637 Effective length of database: 412 Effective search space: 262444 Effective search space used: 262444 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: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. 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