Align Lmo2663 protein (characterized, see rationale)
to candidate Echvi_0507 Echvi_0507 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= uniprot:Q8Y414 (343 letters) >FitnessBrowser__Cola:Echvi_0507 Length = 337 Score = 142 bits (357), Expect = 2e-38 Identities = 113/347 (32%), Positives = 162/347 (46%), Gaps = 17/347 (4%) Query: 1 MKAVVKTNPGYDQMELKDVEEPQVYGDKVKIKVAFTGICGSDIHTFKGEYKNPTTPVTLG 60 MK + T PG E + E+P + + IK+ GICG+D+H ++G P LG Sbjct: 1 MKILTCTEPG--NFEYSEGEKPTLSPGRAIIKIKRIGICGTDLHAYEGTQPFFNYPRVLG 58 Query: 61 HEFSGVVVEVGPDVTSIKVGDRVTSETTFETCGECIYCKEHDYNLCSNRRGIGTQANGSF 120 HE SG +VEV GD VT F CGEC+ CK N C+ G +G Sbjct: 59 HELSGELVEV-DGAEGFVPGDLVTIIPYF-NCGECVACKAGKPNCCATISVFGVHEDGGM 116 Query: 121 AEFVLSREESCHVLDERISLEAAALTEPLACCVHSALEKTTIRPDDTVLVFGPGPIGLLL 180 EF+ S S V E +SLE AL EPLA H + + ++P + V+V G GPIGL + Sbjct: 117 KEFI-SVPSSSLVKQEGLSLEQLALAEPLAIGAH-GVRRAGVQPGEFVVVMGAGPIGLGV 174 Query: 181 AQVVKAQGATVIMAGITKDSDRLRLAKE-LGMDRIVDTLKEDLAEVVLGMTGGYGAERVF 239 + + G VI I + DRL +E LG++ V+ K D + +TGG AE V Sbjct: 175 MEFARIAGGKVIAMDI--NEDRLAFCRETLGVEYTVNA-KGDFKAAIADITGGSFAESVI 231 Query: 240 DCSGAVPAVNQGLPLTKKKGDFVQVGLFAEKKNAID--EESIIQREIAYIGSRSQKPSSW 297 D +G+ A++ G L G +V VGL +K I+ +RE + SR+ + Sbjct: 232 DATGSSVAIHHGFGLMAHGGRYVLVGL---QKGPIEFNHPEFHKRESTLMSSRNATREDF 288 Query: 298 ILALDLLANGKIDTDKMITKVYGLDDWREAFEAVM--AGNEIKVLVK 342 L L K+ IT D + F + + A IK +V+ Sbjct: 289 DTVLKALKEQKVKAASYITHEVAFDQVKADFASWLDPANKVIKAMVR 335 Lambda K H 0.317 0.135 0.392 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: 288 Number of extensions: 17 Number of successful extensions: 5 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: 343 Length of database: 337 Length adjustment: 28 Effective length of query: 315 Effective length of database: 309 Effective search space: 97335 Effective search space used: 97335 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: 49 (23.5 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