Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF3824 PS417_19580 acetyl-CoA carboxylase
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__WCS417:GFF3824 Length = 538 Score = 471 bits (1212), Expect = e-137 Identities = 253/538 (47%), Positives = 330/538 (61%), Gaps = 10/538 (1%) Query: 1 MTVLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRL 60 M V+ S I +F NR AM AIA + A E A+ + RG+LLPR+RL Sbjct: 1 MPVIESLIDTHHAQFAQNREAMLAAIAHLHQLEHTLLAKAQE-AKPKFDKRGQLLPRERL 59 Query: 61 ATLIDPGTPFLEVGATAAYGMYND---DAPGAGLITGIGRISARECMIVCNDPTVKGGTY 117 A L+DPG PFLE+ + A Y +++D A G GLI GIG +S ++V N+ +KGGT Sbjct: 60 ALLLDPGAPFLELASLAGYKLHDDKDGSAAGGGLIAGIGYVSGVRMLVVANNSAIKGGTI 119 Query: 118 YPLTVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHFGRIFYNQANMSAAG 177 P +KK LR Q IA EN+LP V L +SGGANL E+F + R F NQA MSA G Sbjct: 120 SPTGLKKSLRLQHIAMENKLPVVTLAESGGANLNYAAEIFVEG---ARSFANQARMSAMG 176 Query: 178 IPQIAVVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLGGADV 237 +PQI VV GS TAGGAY P +SD ++V + +FLAGPPL++AATGEV + E+LGGA++ Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRGRAKLFLAGPPLLKAATGEVATDEELGGAEM 236 Query: 238 HTRLSGVADHLARDDAHALALARRAVSAL--NREKPWTVERIEPEPPLYDPEEIAGIVPA 295 H +G A++LA +DA + +AR V L N P R EP LY EE+ G++P Sbjct: 237 HAHTAGTAEYLAENDADGVRIARDIVGLLPWNDHLPMVPNRDYAEP-LYPIEELLGLIPD 295 Query: 296 DLKTPYEIREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSESAVK 355 D K PY++RE++ARL DGSRF EFK F VCG H+ G VG++ NNG + + A K Sbjct: 296 DPKKPYDVREILARLADGSRFLEFKGEFDAHTVCGHLHIQGHAVGVIGNNGPITPKGATK 355 Query: 356 GAHFVELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITMLVGG 415 AHF++LC Q R PL+FL N TGFMVG + E +G+ KHGAK++ AVA +VPK+T++VGG Sbjct: 356 AAHFIQLCDQSRTPLLFLHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTIVVGG 415 Query: 416 SFGAGNYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSEEEEA 475 S+GAGNY MCGR PRF++ WPNSR +VMGG QA VL V + G + Sbjct: 416 SYGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVTEAKQLKDGLVPDPKVLD 475 Query: 476 RFRQPVLDLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETRFGLF 533 Q + QS LY SA LWDDG+IDPR +R +L L A + E + F Sbjct: 476 MLEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGFLLDICHEAQVRELQANTF 533 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: 758 Number of extensions: 33 Number of successful extensions: 6 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: 538 Length adjustment: 35 Effective length of query: 500 Effective length of database: 503 Effective search space: 251500 Effective search space used: 251500 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