Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_041096898.1 SUTH_RS02695 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000828635.1:WP_041096898.1 Length = 668 Score = 532 bits (1371), Expect = e-155 Identities = 317/669 (47%), Positives = 408/669 (60%), Gaps = 13/669 (1%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACRVIKTAR+MGI+TVAVYSEAD A V +ADEAVCIG + KESY Sbjct: 1 MFTKILIANRGEIACRVIKTARRMGIRTVAVYSEADAGARHVRLADEAVCIGAPSPKESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 LVADKIIAA TGA+AVHPGYGFLSEN +F+ + G+ FIGP +I MG K E+K Sbjct: 61 LVADKIIAAALATGAQAVHPGYGFLSENEDFAEACAKNGLVFIGPPVSAIRAMGSKSEAK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KL +A V PGY+ P+ + A IGYPV+IKA+AGGGGKG+R A+ + Sbjct: 121 KLMEKAGVPLTPGYHGDNQEPEFLKQQADAIGYPVLIKAAAGGGGKGMRAVDKSADFLDA 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 +SC EA++SFGD V IEKY+ PRHIEIQV GDSHGN VYL ERDCS+QRRHQKV+E Sbjct: 181 LASCKREAQSSFGDQHVLIEKYLQRPRHIEIQVFGDSHGNCVYLFERDCSVQRRHQKVVE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAP+P + PE R AMG+ AV A+AV Y AGTVEF+V+ FYF+EMNTRLQVEHPV Sbjct: 241 EAPAPNMPPERRAAMGKAAVDAAQAVGYVGAGTVEFIVN-QDGTFYFMEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE+ITGLDLVE ++V GE LPL Q + I G A+E RI AEDP +GFLPS G+L+ Sbjct: 300 TEMITGLDLVEWQLKVGAGETLPLRQEQLAIRGHALEARIYAEDPDKGFLPSIGKLIHLA 359 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PPAE VRVDTGV EIS +YD MIAKLIV +RE+A+ARM AL + + G+S+ Sbjct: 360 PPAET-LHVRVDTGVEQDDEISPHYDPMIAKLIVWDETRERALARMLQALADYRVVGVSN 418 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVH-RRYIDR 479 NI F + L+ F DTG I +E F ++ P + L+ +A + ++Y Sbjct: 419 NIGFLSRLVACPAFAQADLDTGLIERERGFLFPETVEPPAEAWLVAALAELIRDQQYALA 478 Query: 480 AAQVSG--QLPGHERKVGDEWVVIRNGERH-PVVAKPIEGGYLVTYNGEKYELLSDWRQG 536 A+ SG P HER D W + N R + A E Y G+ + L ++ Sbjct: 479 EAEASGDPHSPWHER---DGWRLNGNARREIKLRAGETEKVVNAGYAGDSFTL--EFEGQ 533 Query: 537 QSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMV--MSARAAELLALMPEKAAPDLS 594 + G G E + + R+ + + + + + A + L + Sbjct: 534 TTAATGRFAGSELRVDLGGRRINVTVVAANEKRHVFIDGICFVFAAIDPLFHAGSGGGAE 593 Query: 595 KFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLS 654 L +PMPG + + VG +V+ G L ++EAMKME+ + A +K G +S Sbjct: 594 GGLTAPMPGKIIALIAEVGGKVEKGAPLLILEAMKMEHTITAPAAGTIKAFRFNVGEQVS 653 Query: 655 VDEIIIEFE 663 ++EFE Sbjct: 654 DGAELVEFE 662 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: 1134 Number of extensions: 45 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: 663 Length of database: 668 Length adjustment: 38 Effective length of query: 625 Effective length of database: 630 Effective search space: 393750 Effective search space used: 393750 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 Apr 09 2024. 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