Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011386591.1 AMB_RS21445 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000009985.1:WP_011386591.1 Length = 663 Score = 866 bits (2238), Expect = 0.0 Identities = 437/662 (66%), Positives = 519/662 (78%), Gaps = 1/662 (0%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACRVIKTA+KMGIKTVAVYS+ADKDAL V MADEAV IGPAAS +SY Sbjct: 1 MFTKILIANRGEIACRVIKTAKKMGIKTVAVYSDADKDALHVSMADEAVHIGPAASAQSY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 LV DKI+ ACKQTGA+AVHPGYGFLSE EF L + GI FIGP ++I MGDKIESK Sbjct: 61 LVIDKIVDACKQTGAQAVHPGYGFLSEKREFQEALGKAGIAFIGPDAHAIFAMGDKIESK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KLA EA VNT+PGY I D AV+IA++IGYPVM+KASAGGGGKG+R+A+NDAEAHEG Sbjct: 121 KLAREAGVNTVPGYLGVIKDADEAVKIAREIGYPVMLKASAGGGGKGMRLAWNDAEAHEG 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 F+S NEA+ SFGDDRVF+EK++ +PRHIEIQVL D G +YL ER+CSIQRRHQKVIE Sbjct: 181 FTSATNEAKTSFGDDRVFVEKFIEQPRHIEIQVLADGQGTTLYLGERECSIQRRHQKVIE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAPSPF+ PE RKAMGEQA ALAR VNY+SAGTVEF+V GAT EFYFLEMNTRLQVEHPV Sbjct: 241 EAPSPFLTPETRKAMGEQACALARIVNYKSAGTVEFIVGGATGEFYFLEMNTRLQVEHPV 300 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE+ITGLDLVEQMIRVA GEKL +TQ DV++NGW+ME R+ AEDPFR FLPSTGRL ++Q Sbjct: 301 TEMITGLDLVEQMIRVASGEKLSITQDDVKLNGWSMEARVYAEDPFRNFLPSTGRLTRYQ 360 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PPAE VRVDTGVY+GGEISM+YD MIAKLI +G +R+ AIA MR AL+ + IRG+S Sbjct: 361 PPAE-SAHVRVDTGVYEGGEISMFYDPMIAKLITYGPTRDAAIAHMRQALDEYYIRGLSH 419 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRA 480 NIPF A+L RF G T FIA+EY GF A+ +P DDP +LI VAA +RR +R Sbjct: 420 NIPFLASLFSKERFVKGALTTNFIAEEYANGFHANDLPADDPTVLIAVAAAANRRIHERD 479 Query: 481 AQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLF 540 ++SGQ PGHE K GDEWVV+ +G+ H + +P E GY V GE ++ +DW+ G+ LF Sbjct: 480 TRISGQFPGHEMKAGDEWVVVMSGQYHDITVRPAENGYAVALGGETVDVRTDWQIGEPLF 539 Query: 541 NGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSP 600 +G +Q+ER +L H G+R D++V++ AA++ LMP KA PD+SK+LLSP Sbjct: 540 RANVDGRAVAVQIERVGSGLRLAHAGSRVDVLVLTPHAAKMNKLMPFKAPPDMSKYLLSP 599 Query: 601 MPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIII 660 MPGLL ++ V GQEVKAGE LAV+EAMKMENILKAE+D V K +G SL+VD+ II Sbjct: 600 MPGLLVKLLVEAGQEVKAGEPLAVVEAMKMENILKAERDATVAKTHAASGDSLAVDQKII 659 Query: 661 EF 662 EF Sbjct: 660 EF 661 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: 1216 Number of extensions: 51 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: 663 Length of database: 663 Length adjustment: 38 Effective length of query: 625 Effective length of database: 625 Effective search space: 390625 Effective search space used: 390625 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