Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_011766793.1 AZO_RS15410 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000061505.1:WP_011766793.1 Length = 666 Score = 540 bits (1392), Expect = e-158 Identities = 329/674 (48%), Positives = 414/674 (61%), Gaps = 22/674 (3%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MF KILIANRGEIACRVIKTAR+MGIKTVAVYSEAD +A V +ADEAV IGPAA++ESY Sbjct: 1 MFNKILIANRGEIACRVIKTARRMGIKTVAVYSEADANARHVRLADEAVLIGPAAARESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 LV D+IIAA K TGA+A+HPGYGFLSEN +F E EGI FIGP +I MG K E+K Sbjct: 61 LVIDRIIAAAKATGAQAIHPGYGFLSENEDFCEACEREGIVFIGPPVSAIRAMGSKSEAK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KL A+V PGY+ P A IGYPV+IKA+AGGGGKG+R+ + + Sbjct: 121 KLMEAARVPLTPGYHGDNQEPAFLHRQADGIGYPVLIKAAAGGGGKGMRLVEKSEDFIDA 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 +SC EA +SFGDD V +EKY+ PRHIEIQV GDSHGN VYL ERDCS+QRRHQKV+E Sbjct: 181 LASCKREAISSFGDDHVLVEKYITRPRHIEIQVFGDSHGNCVYLFERDCSVQRRHQKVLE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAP+P + E R AMG+ AV ARAV Y AGTVEF+ + FYF+EMNTRLQVEHPV Sbjct: 241 EAPAPGMTAERRAAMGKAAVEAARAVGYVGAGTVEFIAN-QDGSFYFMEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TE+ITGLDLVE +RVA GEKLPL Q +QI G A+E RI AEDP +GFLPSTG+LV Sbjct: 300 TEMITGLDLVEWQLRVASGEKLPLAQEQLQIRGHALEARIYAEDPAKGFLPSTGKLVHLA 359 Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420 PPAE VRVDTGV +G EIS +YD MIAKLIV +R++A+ARM AL + + G+++ Sbjct: 360 PPAE-GLHVRVDTGVEEGDEISPHYDPMIAKLIVWDINRDRALARMLQALADYRVVGVAN 418 Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDD--PALLIGVAAFVH----R 474 NI F + L F + DTG I +E A + P D PA + VAA R Sbjct: 419 NIEFLSRLTACPAFATADLDTGLIERER-----AYLFPEGDAIPAEVWRVAALAELLRDR 473 Query: 475 RYIDRAAQVSGQLPGHERKVGDEWVVIRNGERHPVV-AKPIEGGYLVTYNGEKYELLSDW 533 RY + AQ G+ P D W + + R+ V A + V+Y + L D Sbjct: 474 RYGEEKAQ-RGRDPLSPWHARDGWRMNASARRNLVFRAGEAQQTVSVSYRANGFALTVDG 532 Query: 534 RQGQSLFNGTCNGEEFT-LQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPD 592 + G N + + RM + G + + + R+ +L ++ P A + Sbjct: 533 NTVSA--RGELNPRGLLHVDFDGARMDATVIAAGEKRHIF-LHGRSWQLASVDPLHHAGE 589 Query: 593 ---LSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTA 649 LL+PMPG + + G +V+ G L ++EAMKME+ + A VK Sbjct: 590 GGGAEGGLLAPMPGKVIALLAEAGAKVEKGAPLLILEAMKMEHTITAPATGTVKGFRFAV 649 Query: 650 GSSLSVDEIIIEFE 663 G + ++EFE Sbjct: 650 GDQVGDGAELVEFE 663 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: 1112 Number of extensions: 43 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 663 Length of database: 666 Length adjustment: 38 Effective length of query: 625 Effective length of database: 628 Effective search space: 392500 Effective search space used: 392500 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 24 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