Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_041100195.1 SUTH_RS14320 biotin carboxylase N-terminal domain-containing protein
Query= metacyc::MONOMER-13589 (666 letters) >NCBI__GCF_000828635.1:WP_041100195.1 Length = 662 Score = 480 bits (1235), Expect = e-139 Identities = 286/680 (42%), Positives = 389/680 (57%), Gaps = 45/680 (6%) Query: 2 FKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSYI 61 F KIL+ANRGEIACR+++TAR +G +TVAVYSDAD NA HV++ADEA+ IGP PA SY Sbjct: 4 FSKILVANRGEIACRIMRTARTLGYRTVAVYSDADANAPHVALADEAVRIGPAPAVDSYR 63 Query: 62 VIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSKK 121 ++ A +ASGA+A+HPGYGFLSE DFA A AG+VFIGPP+ AI AMGDK +K+ Sbjct: 64 NSVALLAAARASGAQALHPGYGFLSENADFARACVEAGLVFIGPPADAISAMGDKAGAKR 123 Query: 122 LAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEGF 181 AGV T PGY+ + + + ++G+P+++KA AGGGG+GMR+A + ++ E Sbjct: 124 RMIAAGVPTAPGYLDEDQSDERLIAEAEKLGFPLLVKAVAGGGGRGMRLAQNASDFPEAL 183 Query: 182 ESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIEE 241 ++ EA +FGD + +E+ + Q RHIEIQ+ AD HGN V+L ER+C+ QRR QKVIEE Sbjct: 184 AGARREALAAFGDATLMLERLIPQGRHIEIQIFADAHGNAVHLGERDCTTQRRRQKVIEE 243 Query: 242 APSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVTE 301 APSP + A R+ MG A A A AVGY AGTVEFIVD + YFLEMNTRLQVEHPVTE Sbjct: 244 APSPIVTPAMRETMGRDAVAAALAVGYRGAGTVEFIVDQELRHYFLEMNTRLQVEHPVTE 303 Query: 302 LITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRPP 361 +ITG DLVE +RVAAGE LP +Q +++ +G A+E+RLYAEDPY F P G + +RP Sbjct: 304 MITGQDLVEWQLRVAAGEALPLRQDEIRFSGHAIEARLYAEDPYAGFAPQTGPVLHFRP- 362 Query: 362 VESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGIG 421 S VR D+G+ EGG ++ +YDPM+AK+ R+ AI + AL+ + G+ Sbjct: 363 --EAALRSGVRIDSGIAEGGAVTPFYDPMVAKVIAHGRDRKDAIRRLMAALEDAPLLGLP 420 Query: 422 HNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEIR 481 N + ++DH F + D+ T+ + E +G A+L PT AA E Sbjct: 421 TNGRLLRDLVDHGSFRRADMHTSLLDEWAANG--EAILQRPTPTEDDWQLAAAMFAGEPG 478 Query: 482 RTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSD--WTPG 539 S G D ++A GE+ + I +G S+RV + PG Sbjct: 479 WRATSA--------AGFDLILACDGETRKLRIGL----------EGDSVRVGAAPLCVPG 520 Query: 540 QPLASLMV---------DGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALLMPE 590 PL + D L +G + + G L + +A + E Sbjct: 521 TPLRGQVTATDLRIESEDHGRLRYTIGGVTRHAIIHRDGDTLHL-----ARAAAIFVFTE 575 Query: 591 KLPPDTSKYLLCP------MPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGT 644 P + LL P + G V ++ V GD V GQ LA +EAMKME + A GT Sbjct: 576 ASPFPVVEILLDPRNARAAVAGTVARLEVGAGDTVIAGQTLAVIEAMKMEMRVTANAAGT 635 Query: 645 VKKIAAAPGASLRVDDVIME 664 V I G + +++E Sbjct: 636 VAAIRVLAGQQVAAGAILVE 655 Lambda K H 0.318 0.134 0.386 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: 1078 Number of extensions: 54 Number of successful extensions: 3 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: 666 Length of database: 662 Length adjustment: 38 Effective length of query: 628 Effective length of database: 624 Effective search space: 391872 Effective search space used: 391872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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