Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS29410 RR42_RS29410 acetyl-CoA carboxylase
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS29410 Length = 540 Score = 450 bits (1158), Expect = e-131 Identities = 241/520 (46%), Positives = 322/520 (61%), Gaps = 10/520 (1%) Query: 1 MTVLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRL 60 M + S +S SE F+ANRA M + I A AA +RER RG+LLPRDRL Sbjct: 1 MANIESRLSAGSEAFQANRAGMLALLERIR-AFEQRAASLSAASRERFEKRGQLLPRDRL 59 Query: 61 ATLIDPGTPFLEVGATAAYGMYNDD----APGAGLITGIGRISARECMIVCNDPTVKGGT 116 A L+DPG PF+E+ + A G+ N D PG GLI GIG +S CMI +D + G Sbjct: 60 ALLLDPGAPFIELSSLAGLGLDNPDLDKSVPGGGLIAGIGFVSGLRCMISASDSGINAGA 119 Query: 117 YYPLTVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAA 176 P + K LR QEIA EN+LP V LV+S GANL D G +F N A +SAA Sbjct: 120 LQPKGLDKQLRVQEIALENKLPYVQLVESAGANLMTYK--VEDFVRGGNLFRNLALLSAA 177 Query: 177 GIPQIAVVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGAD 236 G+P + V GS TAGGAY +SD I+V + FLAGPPL+ AATGEV + E+LGGA Sbjct: 178 GLPVVTVTHGSSTAGGAYQTGLSDYIIMVRGRSRAFLAGPPLLMAATGEVATEEELGGAV 237 Query: 237 VHTRLSGVADHLARDDAHALALARRAVSALN--REKPWTVERIEPEPPLYDPEEIAGIVP 294 +HT +SG+ D+LA DD AL +AR + ++ R++P R +PP +D EE+ G++P Sbjct: 238 MHTSVSGLGDYLAEDDRDALRIAREILGKIDWHRDQPAAAPR-SYKPPRFDAEELLGVMP 296 Query: 295 ADLKTPYEIREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAV 354 D K P +++EVIAR+ D S F EF +G VCG + G P+GI+ NNG + A Sbjct: 297 MDHKRPVDMKEVIARIADDSDFLEFGENYGGATVCGHVKIEGWPLGIITNNGPIDPAGAT 356 Query: 355 KGAHFVELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVG 414 K HF++ C Q R P+++L N TGFMVGR +E GI KHG+K++ AV+ VP+IT+ G Sbjct: 357 KATHFIQACCQSRTPILYLNNTTGFMVGRSHEEAGIIKHGSKMIQAVSNATVPQITIYCG 416 Query: 415 GSFGAGNYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEE 474 SFGAGNYGMCGR F PRF ++WPN++ +VMGGEQAA ++ V A+KR G ++ Sbjct: 417 ASFGAGNYGMCGRGFHPRFCFSWPNAKTAVMGGEQAARTMAIVTEAAMKRKGGQADADQL 476 Query: 475 ARFRQPVLDLFERQSHPLYASARLWDDGVIDPRKSRDVLA 514 ++ +++ F+RQ SA + DDGVIDPR +R VLA Sbjct: 477 EALQKGIVERFDRQMSVFVTSAHVLDDGVIDPRNTRAVLA 516 Lambda K H 0.320 0.136 0.404 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: 736 Number of extensions: 33 Number of successful extensions: 5 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: 535 Length of database: 540 Length adjustment: 35 Effective length of query: 500 Effective length of database: 505 Effective search space: 252500 Effective search space used: 252500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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