Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate Ac3H11_1923 Geranyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.5)
Query= metacyc::MONOMER-17283 (535 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1923 Length = 537 Score = 413 bits (1061), Expect = e-119 Identities = 240/543 (44%), Positives = 322/543 (59%), Gaps = 17/543 (3%) Query: 2 SIIHSHIQPNSPDFQANFAYHQSLAADLRERLAQIRQGGGAEQRRRHEERGKLFVRDRID 61 ++ S P S + A Q+ LR L + A + E+RG+L R R+ Sbjct: 3 AVFTSRFNPGSAEATQRRAALQARLDALRA-LEERAAAASARSLPQFEKRGQLLPRQRVA 61 Query: 62 TLIDPDSSFLEIGALAAY--NVYDEE--VPAAGIVCGIGRVAGRPVMIIANDATVKGGTY 117 L+D + +L + LA Y +V D E VP G+V GIG V+G M++A+D+ ++ G Sbjct: 62 LLLDAGAPWLPLCTLAGYLQDVKDPEKSVPGGGMVAGIGFVSGVRCMVVASDSGIEAGAI 121 Query: 118 FPLTVKKHLRAQEIARENRLPCIYLVDSGGAYLP-LQSEVFPDRDHFGRIFYNQAQMSAE 176 P+ ++K LR QEIA +NRLP I+LV+S GA L + E F H G +F N A++SA Sbjct: 122 QPMGLEKILRVQEIALQNRLPFIHLVESAGANLMRYRVEGFV---HGGTLFRNLARLSAA 178 Query: 177 GIPQIACVMGSCTAGGAYVPAMSDEVVIVKGNGTIFLGGPPLVKAATGEEVTAEELGGAD 236 GIP I GS TAGGAY+P +SD V++V+G FL GPPL+KAATGE T EELGGA+ Sbjct: 179 GIPVITVQHGSGTAGGAYMPGLSDVVIMVQGRSRAFLAGPPLLKAATGEIATEEELGGAE 238 Query: 237 VHTRISGVADYFANDDREALAIVRDIVAHLGPRQRANWELRDPEP-PRYDPREIYGILPR 295 +HT +SG+ +Y A DDREA+ + RD+VA LG N R P P ++ ++ Sbjct: 239 MHTAVSGLGEYLAQDDREAIGLARDVVAQLG----WNMPRRPSAPVPLLPADDLLSLMSA 294 Query: 296 DFRQSYDVREVIARIVDGSRLHEFKTRYGTTLVCGFAHIEGFPVGILANNGILFSESALK 355 D RQ D+REV+AR+VDGS L EFK RYG VC HI G VG ++NNG + A K Sbjct: 295 DLRQPVDMREVMARLVDGSELLEFKARYGMATVCAQGHIGGHAVGFISNNGPIDVAGANK 354 Query: 356 GAHFIELCCARNIPLVFLQNITGFMVGKQYENGGIAKDGAKLVTAVSCANVPKFTVIIGG 415 HFI+ C P+++LQN TG+MVGK E GG+ K G+K++ AV+ A VP+ T+ G Sbjct: 355 ATHFIQWMCQLGHPIIYLQNTTGYMVGKDSEQGGMIKHGSKMIQAVTNATVPQITIQCGA 414 Query: 416 SFGAGNYGMCGRAYQPRQLWMWPNARISVMGGTQAANVLLTIRRDNLRARGQDMTPEEQE 475 SFGAGNYGMCGR Y PR L+ WP A+ +VMGG QAA + + L +G P E + Sbjct: 415 SFGAGNYGMCGRGYAPRFLFSWPGAKTAVMGGEQAARTMQIVTEAALARKGITPDPAESQ 474 Query: 476 RFMAPILAKYEQEGHPYYASARLWDDGVIDPVETRRVLALGLAAAAEA---PVQPTRFGV 532 I+A +E + +Y S L DDGVIDP +TR VLA L AEA ++P FGV Sbjct: 475 AQFDKIVAMFEAQADVFYTSGLLLDDGVIDPRDTRAVLAFCLDTCAEAQARTLRPLSFGV 534 Query: 533 FRM 535 RM Sbjct: 535 ARM 537 Lambda K H 0.322 0.139 0.423 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: 731 Number of extensions: 37 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: 537 Length adjustment: 35 Effective length of query: 500 Effective length of database: 502 Effective search space: 251000 Effective search space used: 251000 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 (21.9 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