Align Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4) (characterized)
to candidate Pf1N1B4_222 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
Query= reanno::psRCH2:GFF1050 (535 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_222 Length = 538 Score = 463 bits (1191), Expect = e-135 Identities = 253/541 (46%), Positives = 335/541 (61%), Gaps = 11/541 (2%) Query: 1 MAILHTQINIRSPEFAANSAAMLEQVNDLRALLGRVSEGGGATAQQRHVSRGKLLVRERI 60 M ++ +Q++ S FA N AAML + +R L + A A+ R RG+LL RER+ Sbjct: 1 MPVIQSQVDPFSESFARNRAAMLAGIEQVRQLEQNL-RSKAAEAKPRFDKRGQLLPRERL 59 Query: 61 DTLLDAGSAFLELAPLAAHEVYGE---DVAAAGVVAGIGRVEGIECMIIANDATVKGGTY 117 + LLD G+ FLELA LA ++++ + A G++AGIG V G +++AN++ +KGGT Sbjct: 60 NLLLDPGAPFLELASLAGYKLHDDKDGSSAGGGLIAGIGYVSGARVLVVANNSAIKGGTI 119 Query: 118 YPLTVKKHLRAQTVARENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAMG 177 P +KK LR Q +A ENRLP I L +SGGANL E+F + R F NQA MSAMG Sbjct: 120 SPSGLKKSLRLQQIAMENRLPVITLAESGGANLNYAAEIFVEG---ARSFANQARMSAMG 176 Query: 178 IPQIAVVMGSCTAGGAYVPAMADETIMVRNQATIFLAGPPLVKAATGEVVTAEELGGADV 237 +PQI VV GS TAGGAY P ++D ++VR +A +FLAGPPL+KAATGEV T EELGGA + Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRGKAKLFLAGPPLLKAATGEVATDEELGGAQM 236 Query: 238 HCKTSGVADHYAENDEHALSIARRCVANLNWR-KLGQLQTREPRAPLYAADELYGVIPAQ 296 H +T+G A++ AEND + R ++ L W +L L R PLY DEL G+IP Sbjct: 237 HAQTAGTAEYLAENDADGVRQVREIMSLLPWNDQLPWLPERRWEEPLYPIDELLGLIPDD 296 Query: 297 AKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKG 356 K+PYDVRE+IAR+ D S F EFK F +CG L G + NNG + + A K Sbjct: 297 PKKPYDVREIIARIADASNFLEFKGEFDQQTICGHLQLQGRACGFIGNNGPITPKGASKA 356 Query: 357 AHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAQVPKFTVLIGGS 416 A FI+L Q PLLF N TGFMVG + E G+ KHGAK++ AVA A+VPK T+++GGS Sbjct: 357 AQFIQLCDQSQTPLLFFHNTTGFMVGTESEQQGVIKHGAKMIQAVANARVPKLTIVVGGS 416 Query: 417 FGAGNYGMCGRAYDPRFLWMWPNARIAVMGGEQAAGVLAQVKQEQSERAGKSLGDDEVAA 476 +GAGNY MCGR DPRF++ WPN+R AVMGG QA VL V + + + G + Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSRTAVMGGAQAGKVLRIVTEAKQLKDGLVPDPKMLDM 476 Query: 477 IKQPILEQYERQGHPYYSSARLWDDGVIDPAQTREVLGLALSAALNAPI---EPTRFGVF 533 ++Q ++ + Q Y SA LWDDG+IDP TR +LG L A + +P FGV Sbjct: 477 LEQVTAQKLDSQSTALYGSANLWDDGLIDPRDTRTLLGYLLDICHEAEVRSLQPNSFGVA 536 Query: 534 R 534 R Sbjct: 537 R 537 Lambda K H 0.321 0.136 0.405 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: 753 Number of extensions: 38 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: 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