Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate SMc02852 SMc02852 hypothetical protein
Query= SwissProt::Q9JYL2 (381 letters) >FitnessBrowser__Smeli:SMc02852 Length = 464 Score = 75.9 bits (185), Expect = 2e-18 Identities = 109/437 (24%), Positives = 169/437 (38%), Gaps = 83/437 (18%) Query: 5 QSLELAKELISRPSVTPDDR---DCQKLLAERLHKIGFAAEELHFGDTKNIWL------R 55 QSLE +L+ S++ D +C+K + ++G E DT + Sbjct: 18 QSLERLFDLVRIKSISTDPAFKAECRKAAEWLVAELGTLGFEASVRDTPGHPMVVAHHAA 77 Query: 56 RGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERD---GR--LYGRGAADMKTSIACFV 110 AP + F GH DV P P+ W++PPFEP+ R+ GR + GRG AD K + FV Sbjct: 78 GKADAPHLLFYGHYDVQPVDPLNLWETPPFEPSLREVEPGRKIITGRGTADDKGQLMTFV 137 Query: 111 TACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKAR--DELIDYCIVGEPTAV 168 A V + +G + IT EG+ G+ + L+A + DY +V + + Sbjct: 138 EA----VRAYKEARGVLPCRITILFEGEEESGSPSLKPFLEANAGELKADYALVCDTSMW 193 Query: 169 DKLGDMIKNGRRGSLSGNLTVKG--KQGHIAY-PHLAINPVHTFA--------------- 210 D+ I G RG + + VK + H Y A NP+H A Sbjct: 194 DRETPAISAGLRGLVGEEVVVKAADRDLHSGYFGGAAANPIHILAEILAGLHDETGRVTL 253 Query: 211 ----------PALLELTQEVWDEGNEYF-----------------------PPTSFQISN 237 PA ++ T E + E F PT+ +I+ Sbjct: 254 DDFYEGVEETPAEIKATWETLGQTAEKFLGEIGLSIPSGERGRSVLELTWARPTA-EING 312 Query: 238 ING---GTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHA-ILDKHGVQYDLQWSCSGQ 293 I G G G VI E + K +FR + A +++ A + K +++ G Sbjct: 313 ITGGYTGEGFKTVIAAEASAKVSFRLVGKQDPARIRESFRAYVRSKIPADCSIEFHAHGG 372 Query: 294 P---FLTQAGKLTDVARAAIAETCGIEAELSTTGGTSD--GRFIKAIAQE--LIELGPSN 346 L L A+AA+++ A + GG+ G F + + E L+ G S+ Sbjct: 373 SPAIHLPYDSALLTTAKAALSDEWPKPAVVIGMGGSIPIVGDFQRMLGMESLLVGFGLSD 432 Query: 347 ATIHQINENVRLNDIPK 363 IH NE L K Sbjct: 433 DRIHSPNEKYELTSFHK 449 Lambda K H 0.317 0.135 0.400 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: 420 Number of extensions: 23 Number of successful extensions: 2 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: 381 Length of database: 464 Length adjustment: 32 Effective length of query: 349 Effective length of database: 432 Effective search space: 150768 Effective search space used: 150768 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 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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