Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Pf6N2E2_2411 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
Query= reanno::PS:Dsui_0516 (663 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2411 Length = 656 Score = 481 bits (1239), Expect = e-140 Identities = 296/676 (43%), Positives = 400/676 (59%), Gaps = 40/676 (5%) Query: 2 FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61 F KILIANRGEIACR+ +TA+ +G +TVAV+SEAD DAL V MADEAV IGPAA+++SYL Sbjct: 4 FSKILIANRGEIACRIQRTAQALGYRTVAVFSEADADALHVRMADEAVLIGPAAAQQSYL 63 Query: 62 VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121 I+ A ++ GA+A+HPGYGFLSENA F++ E I FIGP +I MG K +K Sbjct: 64 NPSAILDAARRCGADAIHPGYGFLSENAGFAKACEAADIVFIGPSPEAIDLMGSKRRAKI 123 Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181 IEA V I GY A D A +IGYP+MIKASAGGGG+G+R+ + E Sbjct: 124 AMIEAGVPCIAGYQGAAQDDDTLQREAGRIGYPLMIKASAGGGGRGMRLVQRAEDLLEQL 183 Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241 +EA + FG D + +E+ +++PRH+E+Q+ GD HG ++L ERDCSIQRRHQKVIEE Sbjct: 184 RGARSEALHGFGSDELILEQALIDPRHVEVQIFGDHHGQLIHLGERDCSIQRRHQKVIEE 243 Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301 AP P + ++R+AMG+ A+ ARAVNY AGTVEF+++ A FYFLEMNTRLQVEHPVT Sbjct: 244 APCPVMTTDLRRAMGDAALKAARAVNYVGAGTVEFLLA-ADGRFYFLEMNTRLQVEHPVT 302 Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361 ELITGLDLV + VA G LPL Q V ++G AM+ R+ AEDP FLP TGRL+ ++P Sbjct: 303 ELITGLDLVAWQLDVAAGRSLPLRQEQVTLSGHAMQVRLYAEDPAADFLPQTGRLIGWEP 362 Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421 P++ DG VR+D G+ +G I+ +YDSM+ KLIVHGA+RE+A ++ A+ V+ G+ SN Sbjct: 363 PSQ-DG-VRIDHGLLEGQAITPFYDSMLGKLIVHGATREEARRKLLRAVEDCVLLGVQSN 420 Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPA--LLIGVAAFVHRRYIDR 479 L+ H RF G F GFI + + A++ P + A L I AAF Y Sbjct: 421 QRLLTGLLAHPRFIDGDFGNGFIGQHFAD--HAALRPLEPSAEQLAIATAAF----YQAS 474 Query: 480 AAQVSGQLPGHERKVGDEWVVIRN----GERHPVVAKPIE--GGYLVTYNGEKYELLSDW 533 A+ + L G +G VV+ GE ++ E G + + G EL Sbjct: 475 QARHAQGLGGWRNSIG---VVLHYRIGVGEHDWTLSLVAEADGTFNIRSAGRLIEL---- 527 Query: 534 RQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDL 593 L + +G + R R ++L D+ + + L L AP Sbjct: 528 ----RLLDAAPHGATLVIDGIRRRHAWRL----DGNDLWLFTCPGG--LHLQDRTLAPIA 577 Query: 594 SK------FLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISV 647 +K L +PM G + E+ V G V G+ L V+EAMKME+ LKA D V + V Sbjct: 578 AKTSASDGTLKAPMDGAIVELRVREGSTVHQGQLLMVLEAMKMEHPLKAGVDGVVTHLQV 637 Query: 648 TAGSSLSVDEIIIEFE 663 G + ++++ E Sbjct: 638 ARGDQVKKRQVLLRVE 653 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: 1025 Number of extensions: 44 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: 2 Length of query: 663 Length of database: 656 Length adjustment: 38 Effective length of query: 625 Effective length of database: 618 Effective search space: 386250 Effective search space used: 386250 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