Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ac3H11_1923 Geranyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.5)
Query= BRENDA::Q9I297 (535 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1923 Length = 537 Score = 442 bits (1137), Expect = e-128 Identities = 254/548 (46%), Positives = 336/548 (61%), Gaps = 27/548 (4%) Query: 2 AILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARH----SARGKLLVR 57 A+ ++ NP SAE A + +++ALR L E +AA AR RG+LL R Sbjct: 3 AVFTSRFNPGSAEATQRRAALQARLDALRAL-----EERAAAASARSLPQFEKRGQLLPR 57 Query: 58 ERINRLLDPGSPFLELSALAAH--EVYGEE--VAAAGIVAGIGRVEGVECMIVGNDATVK 113 +R+ LLD G+P+L L LA + +V E V G+VAGIG V GV CM+V +D+ ++ Sbjct: 58 QRVALLLDAGAPWLPLCTLAGYLQDVKDPEKSVPGGGMVAGIGFVSGVRCMVVASDSGIE 117 Query: 114 GGTYYPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPR-QDEVFPDREHFGRIFFNQAN 172 G P+ ++K LR Q IAL+NRLP I+LV+S GANL R + E F H G +F N A Sbjct: 118 AGAIQPMGLEKILRVQEIALQNRLPFIHLVESAGANLMRYRVEGFV---HGGTLFRNLAR 174 Query: 173 MSARGIPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEEL 232 +SA GIP I V GS TAGGAY+P +SD +MV+ ++ FLAGPPL+KAATGE+ + EEL Sbjct: 175 LSAAGIPVITVQHGSGTAGGAYMPGLSDVVIMVQGRSRAFLAGPPLLKAATGEIATEEEL 234 Query: 233 GGADVHCKVSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAPRAP--LYPAEELY 290 GGA++H VSG+ ++ A+DD A+ +AR VA L W R P AP L PA++L Sbjct: 235 GGAEMHTAVSGLGEYLAQDDREAIGLARDVVAQLGWNMP-----RRPSAPVPLLPADDLL 289 Query: 291 GVIPADSKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFA 350 ++ AD +QP D+REV+ARLVDGSE EFKA +G VC H+ G+ + ++NNG + Sbjct: 290 SLMSADLRQPVDMREVMARLVDGSELLEFKARYGMATVCAQGHIGGHAVGFISNNGPIDV 349 Query: 351 EAAQKGAHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFT 410 A K HFI+ CQ G P+++LQN TG+MVG+ E GG+ KHG+K++ AV A VP+ T Sbjct: 350 AGANKATHFIQWMCQLGHPIIYLQNTTGYMVGKDSEQGGMIKHGSKMIQAVTNATVPQIT 409 Query: 411 VLIGGSFGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLG 470 + G SFGAGNYGMCGR Y PRFL+ WP A+ VMGGEQAA + V R G Sbjct: 410 IQCGASFGAGNYGMCGRGYAPRFLFSWPGAKTAVMGGEQAARTMQIVTEAALARKGITPD 469 Query: 471 VEEEAKIKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEP 527 E I+ +E Q +Y+S L DDGVIDP TR VLA L A + P Sbjct: 470 PAESQAQFDKIVAMFEAQADVFYTSGLLLDDGVIDPRDTRAVLAFCLDTCAEAQARTLRP 529 Query: 528 TAFGVFRM 535 +FGV RM Sbjct: 530 LSFGVARM 537 Lambda K H 0.321 0.137 0.409 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: 705 Number of extensions: 32 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: 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