Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS32750 RR42_RS32750 acetyl-CoA carboxylase
Query= reanno::Smeli:SM_b21122 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS32750 Length = 539 Score = 425 bits (1092), Expect = e-123 Identities = 242/546 (44%), Positives = 320/546 (58%), Gaps = 20/546 (3%) Query: 1 MTVLRSHISPSSEEFKANRAAMTEAIATIEDAVRLAAAGGGETARERHVSRGKLLPRDRL 60 M + S I P+S F + RA M I + A+ A E AR RG LLPR+RL Sbjct: 1 MLPIESRIDPASPAFASQRAGMQALIERLR-ALEQRAVAASERARPSFARRGALLPRERL 59 Query: 61 ATLIDPGTPFLEVGATAAYGMYNDD----APGAGLITGIGRISARECMIVCNDPTVKGGT 116 A L+DP T FL + A YGM + D PG L+ GIG + M+V D + G Sbjct: 60 ARLLDPATAFLPIANLAGYGMDDPDHDTAIPGGSLVAGIGFVRGVRAMVVATDSGIDAGA 119 Query: 117 YYPLTVKKHLRAQEIAAENRLPCVYLVDSGGANLPNQDEVFPDRDHF---GRIFYNQANM 173 K +R QEIA ENRLP ++LV+S GANL D F G IFYN A + Sbjct: 120 MTEGGNLKLMRCQEIALENRLPFIHLVESAGANLRKYRV-----DKFVRGGGIFYNLARL 174 Query: 174 SAAGIPQIAVVMGSCTAGGAYVPAMSDEAIIVEKQGTIFLAGPPLVRAATGEVVSAEDLG 233 SAAG+P I VV GS TAGGAY+P +SD ++V + FLAGPPL++AATGE+ + E+LG Sbjct: 175 SAAGLPVITVVHGSSTAGGAYMPGLSDYVVMVRGRARAFLAGPPLLKAATGEIATDEELG 234 Query: 234 GADVHTRLSGVADHLARDDAHALALARRAVSALNREKPWTVERIEP--EPPLYDPEEIAG 291 GAD+H +SG+A+ LA DD HA+ALAR V++L + P R+ +PP D E+ G Sbjct: 235 GADLHATVSGLAEFLAEDDEHAIALARDVVASL--DWPGVAPRLPQPAQPPRLDAGELDG 292 Query: 292 IVPADLKTPYEIREVIARLVDGSRFDEFKARFGTTLVCGFAHVHGIPVGIVANNGVLFSE 351 ++ D+K P ++ E+I RL D S + FK +GT VCG + G VG ++NNG + Sbjct: 293 VMTLDVKKPVDMLEIIGRLTDDSAWLAFKPDYGTATVCGRGRIEGHAVGFISNNGPIDPA 352 Query: 352 SAVKGAHFVELCAQRRIPLVFLQNITGFMVGRKYETEGIAKHGAKLVTAVATVKVPKITM 411 A K A F++ C Q P+VFLQN TGF+VGR E G+ KHGAK++ A++ VP++T+ Sbjct: 353 GATKAAQFIQACNQSGTPIVFLQNTTGFIVGRASEEAGMIKHGAKMIQALSNSTVPQVTI 412 Query: 412 LVGGSFGAGNYGMCGRAFSPRFLWTWPNSRISVMGGEQAAGVLSSVRGEALKRSGKPWSE 471 G SFGAGN+GMCGR F PRF ++WPN+R +VMGGEQAA L V + +R G E Sbjct: 413 YCGASFGAGNFGMCGRGFRPRFCFSWPNARTAVMGGEQAAMTLEIVARQQAERKGAAVDE 472 Query: 472 EEEARFRQPVLDLFERQSHPLYASARLWDDGVIDPRKSRDVLALSLSAALNAPIEETR-- 529 A+ ++ FERQ+ S L DDGVIDPR +R VLA L+ A A R Sbjct: 473 ARLAQQTGEIVANFERQASAFVTSGLLLDDGVIDPRDTRAVLAFVLATAREAEARTPRAM 532 Query: 530 -FGLFR 534 FG+ R Sbjct: 533 QFGVAR 538 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: 728 Number of extensions: 36 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: 535 Length of database: 539 Length adjustment: 35 Effective length of query: 500 Effective length of database: 504 Effective search space: 252000 Effective search space used: 252000 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