Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate SM_b21124 SM_b21124 methylcrotonoyl-CoA carboxylase biotinylated subunit
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__Smeli:SM_b21124 Length = 662 Score = 495 bits (1274), Expect = e-144 Identities = 292/672 (43%), Positives = 395/672 (58%), Gaps = 30/672 (4%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF K+LIANRGEIACR+I+TAR++GI+TVAVYS+AD DAL V +ADEA+ IG A + ESY Sbjct: 1 MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 L + I+ A + GA+A+HPGYGFLSENA+F+ + E G+ F+GP +I MG K +K Sbjct: 61 LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 L + V +PGY+ + A++IGYPV+IKA AGGGGKG+R + Sbjct: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 + EA ++FGD V +E+Y+ +PRHIE+QV GD HGN V+L ERDCS+QRRHQKVIE Sbjct: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGAT----KEFYFLEMNTRLQV 296 EAP+P + E+R+AMG+ AV A+A+ Y AGTVEF+ FYF+EMNTRLQV Sbjct: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300 Query: 297 EHPVTELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRL 356 EHPVTE ITG+DLVE +RVA GE LP QAD+ +NGWA E R+ AEDP RGFLP+TGRL Sbjct: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360 Query: 357 VKFQPPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIR 416 + P +G RVD+GV G I+ YYD +IAKLIVHG +R A+ R++DAL I Sbjct: 361 TELSFP---EGTSRVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIG 417 Query: 417 GISSNIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDP---ALLIGVAAFVH 473 G +N F L + F+SG DTG I +E + A + P D+ A + A Sbjct: 418 GTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIER-LTAPVAPGDEALALAAIFSTGALDP 476 Query: 474 RRYIDRAAQV-SGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYEL--- 529 R D + + S Q+ G ++ VVI + + V G L Sbjct: 477 NRSTDPWSSLGSWQIWGDAHRM----VVIEHADVRATVTLASRGRDQFAVRAGASTLPVL 532 Query: 530 -LSDWRQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEK 588 L + G L G++ ++ R R LFH G V L + Sbjct: 533 VLDRFEGGARL---EVAGQKRLIRFSRDREALTLFHGGRNLVFHVPD-------GLTGGQ 582 Query: 589 AAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVT 648 ++ L++PMPGL++ V V G V G+ L V+EAMKME L A ++ + + V Sbjct: 583 SSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELTLSASREGTIANVHVA 642 Query: 649 AGSSLSVDEIII 660 G+ +S +++ Sbjct: 643 EGAQVSEGTVLV 654 Lambda K H 0.319 0.135 0.391 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: 1079 Number of extensions: 51 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 663 Length of database: 662 Length adjustment: 38 Effective length of query: 625 Effective length of database: 624 Effective search space: 390000 Effective search space used: 390000 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 (21.7 bits) S2: 54 (25.4 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