Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_041101001.1 SUTH_RS17150 acetyl-CoA carboxylase biotin carboxylase subunit
Query= reanno::PS:Dsui_0516 (663 letters) >NCBI__GCF_000828635.1:WP_041101001.1 Length = 665 Score = 974 bits (2517), Expect = 0.0 Identities = 489/666 (73%), Positives = 565/666 (84%), Gaps = 4/666 (0%) Query: 1 MFKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESY 60 MFKKILIANRGEIACRVIKTARKMGI TVAVYSEADKDA+ VEMADE+VCIGP SKESY Sbjct: 1 MFKKILIANRGEIACRVIKTARKMGIATVAVYSEADKDAMHVEMADESVCIGPPPSKESY 60 Query: 61 LVADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESK 120 L DKIIAACK+TGAEAVHPGYGFLSEN EF+RRLEE GI FIGPKH+S+A MGDKI SK Sbjct: 61 LSIDKIIAACKETGAEAVHPGYGFLSENPEFARRLEESGIIFIGPKHHSMAAMGDKIASK 120 Query: 121 KLAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEG 180 KLA+EAKVNTIPG+N AID P+ AVEIAK IGYPVMIKASAGGGGKGLRVAYN+ EAHEG Sbjct: 121 KLALEAKVNTIPGHNAAIDTPEQAVEIAKGIGYPVMIKASAGGGGKGLRVAYNNKEAHEG 180 Query: 181 FSSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIE 240 F++C EA+N+FGDDR+F+EK+V EPRHIEIQ++GD+HGN +YL+ER+CS+QRRHQKVIE Sbjct: 181 FAACKTEAKNAFGDDRIFVEKFVEEPRHIEIQLIGDAHGNTIYLHERECSLQRRHQKVIE 240 Query: 241 EAPSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPV 300 EAPS F+DP RKAMGEQAVALA+AVNY+SAGTVEFVV G K FYFLEMNTRLQVEHPV Sbjct: 241 EAPSSFIDPATRKAMGEQAVALAKAVNYQSAGTVEFVV-GKDKSFYFLEMNTRLQVEHPV 299 Query: 301 TELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ 360 TELITGLDLVE MIRVA GEKLP TQ V++NGWAMECRINAEDPFRGFLPSTGRLVK+ Sbjct: 300 TELITGLDLVELMIRVAAGEKLPFTQEQVRLNGWAMECRINAEDPFRGFLPSTGRLVKYL 359 Query: 361 PPAEV---DGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRG 417 PP E + VRVDTGVY+GGEISM+YDSMIAKLIVH A+R+QAIARMRDALN FVIRG Sbjct: 360 PPPEAGHGNAGVRVDTGVYEGGEISMFYDSMIAKLIVHAATRDQAIARMRDALNQFVIRG 419 Query: 418 ISSNIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYI 477 ++SNI FQAALMQ+ RF SG F+TG IA++YPKGF+A+ VPHDDPA+L+ VAA +HR+Y+ Sbjct: 420 VASNIAFQAALMQNPRFLSGDFNTGLIAEQYPKGFNAADVPHDDPAMLVAVAAAIHRQYL 479 Query: 478 DRAAQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQ 537 R A +SGQ+PGHE GD++VV E++ +GG+ V++ GE YEL SDW+ G Sbjct: 480 ARNATISGQMPGHEFVPGDDFVVQLGTEQYQARVLKADGGWDVSFAGENYELRSDWQFGD 539 Query: 538 SLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFL 597 L+ GT NG+ +QVER + Y+LFHWG +ADM VMSAR A L ALMP KAAPD+SKFL Sbjct: 540 PLYVGTLNGQSICMQVERRGLVYRLFHWGVQADMQVMSARTAVLKALMPVKAAPDMSKFL 599 Query: 598 LSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDE 657 LSPMPGLL +++V GQEVKAGE LA IEAMKMEN+LKAE+DC V+K+ G SL+VD+ Sbjct: 600 LSPMPGLLTQIAVTAGQEVKAGEILAKIEAMKMENVLKAERDCVVEKLLAMPGESLAVDQ 659 Query: 658 IIIEFE 663 II F+ Sbjct: 660 AIIAFK 665 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: 1330 Number of extensions: 46 Number of successful extensions: 4 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: 665 Length adjustment: 38 Effective length of query: 625 Effective length of database: 627 Effective search space: 391875 Effective search space used: 391875 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