Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate 3607987 Dshi_1395 acetyl-CoA carboxylase, biotin carboxylase (RefSeq)
Query= SwissProt::I3R7G3 (601 letters) >FitnessBrowser__Dino:3607987 Length = 448 Score = 452 bits (1162), Expect = e-131 Identities = 223/449 (49%), Positives = 303/449 (67%), Gaps = 1/449 (0%) Query: 1 MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60 MFSK+L+ANRGEIA+RV+RAC ELG+++VAV+S AD HVR ADEA IGP + SY Sbjct: 1 MFSKILIANRGEIALRVIRACRELGIQSVAVHSTADTDAMHVRMADEAVCIGPPPSPQSY 60 Query: 61 LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120 L ++I A A+AIHPGYGFL+ENA F + V+D T++GP+A+ + +G+K A+ Sbjct: 61 LSIPAIISACEITGAEAIHPGYGFLSENANFVQIVQDHGLTFIGPTAEHIRVMGDKITAK 120 Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180 M++ VP VPG+ E + VA + GYPV +KA GGGGRG+K+ + +++D Sbjct: 121 ETMKNLGVPCVPGSDGGVPDLETARRVAGEIGYPVIVKATAGGGGRGMKLAKTAEDLDEA 180 Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240 F+TA+ EG+A F N VY+EKYL PRHIEVQ+ D G HLGERDCSLQRRHQKV E Sbjct: 181 FQTARSEGKAAFGNPDVYLEKYLSTPRHIEVQVFGDGKGGAVHLGERDCSLQRRHQKVFE 240 Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300 EAPSP + + R RIG+ V +Y AGT+EFL E+GEFYF+E+NTR+QVEH VTE Sbjct: 241 EAPSPVIDAETRARIGKTCAEAVARIDYAGAGTIEFLYENGEFYFIEMNTRLQVEHPVTE 300 Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360 + G+D+VK Q+RVAAG + F Q+++++ GH++E RINAE F P G ++T+ P Sbjct: 301 AIFGVDLVKEQIRVAAGYPMTFKQENLQVRGHAIEVRINAE-KVPAFTPCPGMVTTFHTP 359 Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420 GG+G+RMD A+ G I YDS+I KLIV DR L R RAL E ++G+ T +P Sbjct: 360 GGLGVRMDSALYGGYSIPPYYDSLIGKLIVLAQDRPAALARLNRALGELIVDGIDTTVPL 419 Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERI 449 +L +EA + G +T +L+E L+ +I Sbjct: 420 FHALLAEEAIQTGDYTIHWLEEWLETAQI 448 Lambda K H 0.312 0.132 0.371 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: 610 Number of extensions: 19 Number of successful extensions: 2 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: 601 Length of database: 448 Length adjustment: 35 Effective length of query: 566 Effective length of database: 413 Effective search space: 233758 Effective search space used: 233758 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (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