Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1580 Echvi_1580 Choline dehydrogenase and related flavoproteins
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Cola:Echvi_1580 Length = 580 Score = 284 bits (726), Expect = 8e-81 Identities = 203/593 (34%), Positives = 289/593 (48%), Gaps = 63/593 (10%) Query: 14 YDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYE-TAMKNPWDFKHAGKLTE 72 YD I++GSG GG A+K L+E G V ++E G + + + T ++ PW+ G T Sbjct: 12 YDVIIVGSGAGGGMASKILSEAGFSVAVVEAGADFDPAKEEDRTQLRPPWESPRRGAST- 70 Query: 73 EQKRTHPVQKRDYPYQEANEKWWVNDLEC-PYT--EDKRFDWYRGFHVGGKSLMWGRQSY 129 R+ P+ + + D+E PYT D +FDW+R VGG++ WGR S Sbjct: 71 ----------RNRPFGDFDAAIGGWDIEGEPYTFEGDTKFDWFRSRMVGGRTNHWGRISL 120 Query: 130 RLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMDL 189 R ++F+ DG G +WP+ Y +L P+YD ++ G+ GSKE PDG FLPP Sbjct: 121 RFGPNDFKRKDIDGLGDNWPIGYDDLKPYYDKVDKLIGVFGSKEGIYNEPDGFFLPPP-- 178 Query: 190 NIVEKSVKARIEEHYKRERIMMIG------RVANLTVP-HKGRGNCQYRNLCSRGCPFGA 242 K R+ E Y ++ IG R++ LT P + RG C + N C+R C A Sbjct: 179 -------KPRLHELYIKKGADKIGVPVIPSRLSILTKPINNERGACFFCNQCNRACQAYA 231 Query: 243 YFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVF 302 FS+ + + AM ++ L Y++V + D D KA GV I K + +++V Sbjct: 232 DFSSGTCLVKPAMKKGKVDLYTYAMVRKVTTD-DKGKATGVSYISKVDMKEYKLRSRVVV 290 Query: 303 VNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRR 362 + S S ++LNS S+ HP+GL NGSG +GH L D G G D+ Y Sbjct: 291 LGASACESARIMLNSKSKNHPDGLANGSGMIGHYLHDST-GSDRMGFIPGLLDRKKYNED 349 Query: 363 ANG---IYIPRYQNIGNDKRDYLRGFG--YQGGASRANWQGDVAELSFGADLKQKMTTPG 417 G +Y P +++ N K D+ RG+ Y GG S + + +K + PG Sbjct: 350 GVGGMHVYTPWWED--NSKLDFARGYHIEYWGGMSMPGYGFGFGMETIRQHIKDEFGNPG 407 Query: 418 KWS-----------------MGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKE 460 +G+ G GE +P YEN ID DK+G PVL + + + Sbjct: 408 TSGGYGEGLKKDIRAYFGTMVGMSGRGESIPRYENYCEIDNNTVDKYGIPVLKFNYNWTD 467 Query: 461 NEKKMRVDMMNDAAEMLEKAG--MKNIKTFDNGCY----PGMAIHEMGTARMGNDPKTSV 514 E M + E+L AG + K + Y PG IHE+GT RMGN+PKTSV Sbjct: 468 QEVNQAKHMHDTFEEVLTNAGAVIYGNKPGPDTQYGLLTPGRIIHEVGTTRMGNNPKTSV 527 Query: 515 LNKWNQMHEVNNVFVTDGSCMPSIACQNPSLTFMALTARACDYAVKELKKKNI 567 LN Q HE +N+FV DG S A +NP+ T +AL R DY V ELKKKNI Sbjct: 528 LNSNCQAHECDNLFVVDGGPFVSQADKNPTWTILALAWRTSDYIVSELKKKNI 580 Lambda K H 0.317 0.134 0.421 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: 941 Number of extensions: 52 Number of successful extensions: 6 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: 567 Length of database: 580 Length adjustment: 36 Effective length of query: 531 Effective length of database: 544 Effective search space: 288864 Effective search space used: 288864 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: 53 (25.0 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