Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate WP_089300743.1 CHB84_RS07335 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase
Query= curated2:P09062 (423 letters) >NCBI__GCF_900188115.1:WP_089300743.1 Length = 616 Score = 224 bits (572), Expect = 4e-63 Identities = 158/471 (33%), Positives = 236/471 (50%), Gaps = 58/471 (12%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 + +P++GE + + + W + GD + D+ + ++ TDK E+PSPV+G +L + Q Sbjct: 139 VTLPELGESVTEGTVTRWLKQEGDRVEVDEPLLEISTDKVDTEVPSPVAGTLLEITAQAD 198 Query: 66 EVMAVGSELIRI-EVEGSGNHVDVPQAKPAEVPAA-----------PVAAKPE---PQKD 110 E + VG L I + + PQ + A+ A P A+P+ PQ+ Sbjct: 199 ETVEVGGRLAVIGDAPAAPAAGQQPQHEQAQQEQAQQEQAQQERPQPQQAQPQQAQPQQA 258 Query: 111 VKPAAYQASASHE----AAPIVPRQPGDK-------------PLASPAVRKRALDAGIEL 153 +PAA +S H AAP + G P +P VRK A + GI+L Sbjct: 259 QEPAAAASSGRHATPEPAAPSAGQSGGPSGDGAAPADGTASTPYVTPLVRKLASEHGIDL 318 Query: 154 RYVHGSGPAGRILHEDLDAFM-SKPQSA-----AGQTPNGYARRTDSEQVPVIG------ 201 + GSG GRI +D+ A + +K Q A A Q P G + P Sbjct: 319 NSLQGSGVGGRIRKQDVTAAIEAKQQQAPAAEPAAQGPQGGPSAGSTAPAPPAEDTSGMR 378 Query: 202 --------LRRKIAQRMQDAKRRVAHFSYVEEIDVTALEALRQQLNSKHGDSRG-KLTLL 252 +R IA+R +++ + A + V E+DVT + LR++ + + G KLT L Sbjct: 379 GTTQKANRVRLTIAKRTKESLQNSAQLTQVHEVDVTKIARLREKAKAAFLEREGVKLTFL 438 Query: 253 PFLVRALVVALRDFPQINATYDDEAQIITRHGAVHVGIATQGDNGLMVPVLRHAEAGSLW 312 PF +A V AL+ P +NA D+EAQ IT A H+ +A D GL+ PVL +A +L Sbjct: 439 PFFAKATVEALKQHPNVNAYLDEEAQQITYFDAEHLAVAVDTDRGLISPVLHNAGDLNLA 498 Query: 313 ANAGEISRLANAARNNKASREELSGSTITLTSLGALGGIVSTPVVNTPEVAIVGVNRMVE 372 A I LA R NK EELSG T T+T+LG+ G + TP++N P+ I+GV +V+ Sbjct: 499 GLATRIDDLAKRTRTNKIVPEELSGGTFTVTNLGSNGALFDTPIINQPQSGILGVGAVVK 558 Query: 373 RPVVI---DGQ--IVVRKMMNLSSSFDHRVVDGMDAALFIQAVRGLLEQPA 418 RPVVI DG I +R M L+ ++DHR+VDG DA F+ ++ LE+ A Sbjct: 559 RPVVISDMDGNDTIAIRSMAYLALTYDHRLVDGADAGRFLTTIKHRLEEAA 609 Score = 67.8 bits (164), Expect = 9e-16 Identities = 39/129 (30%), Positives = 67/129 (51%), Gaps = 7/129 (5%) Query: 6 IKMPDIGEGIAQVELVEWFVKVGDIIAEDQVVADVMTDKATVEIPSPVSGKVLALGGQPG 65 + +P++GE + + + W + GD + D+ + ++ TDK E+PSPV+G V + Sbjct: 5 LTLPELGESVTEGTVTRWLKQEGDRVEVDEPLLEISTDKVDTEVPSPVAGTVTRIVATQD 64 Query: 66 EVMAVGSELIRIEVEGSGNHVDVPQAKPAEVPAAPVAAKPEPQKDVKPAAYQASASHEAA 125 + VG+EL I+ +GSG A PAE A + + Q+ V+ A Q +A +A Sbjct: 65 TTVEVGAELAVID-DGSGG-----DAAPAE-QGQQSAPQQQAQQPVEQPAQQPAAEQDAT 117 Query: 126 PIVPRQPGD 134 P+QP + Sbjct: 118 QQAPQQPAE 126 Lambda K H 0.316 0.133 0.376 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: 692 Number of extensions: 33 Number of successful extensions: 6 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: 423 Length of database: 616 Length adjustment: 34 Effective length of query: 389 Effective length of database: 582 Effective search space: 226398 Effective search space used: 226398 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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