Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate H281DRAFT_04480 H281DRAFT_04480 FAD/FMN-containing dehydrogenase
Query= BRENDA::H6LBS1 (466 letters) >FitnessBrowser__Burk376:H281DRAFT_04480 Length = 474 Score = 192 bits (488), Expect = 2e-53 Identities = 143/425 (33%), Positives = 215/425 (50%), Gaps = 21/425 (4%) Query: 55 EEVSKIMKYAYEHNIPVVVRGSGTGLVGACVPLFGGIMLETTL--MNNILELDTENLTVT 112 +EV+ ++K A EH I VV +G TGL G P G +L +N + ++D N T+T Sbjct: 51 DEVAALVKLAVEHGIAVVPQGGNTGLAGGATPDSSGAQAVVSLRRLNRVRDIDPHNNTIT 110 Query: 113 VEPGVLLMELSKFVEENDLFYPPD-PGEKSATIAGNISTNAGGMRAVKYGVTRDYVRGLT 171 VE GV+L E+ K EE +P E S TI GN++TNAGG ++YG TR+ GL Sbjct: 111 VEAGVILAEVQKRAEEAGRLFPLSLAAEGSCTIGGNLATNAGGTGVLRYGNTRELCLGLE 170 Query: 172 VVLANGEIIELGGKIVKNSSGYSLKDLVIGSEGTLCVITKAILKLLPLPKMTLSLLIPFE 231 VV GE+ + + K+++GY L+DL IG+EGTL +IT A+LKL P P ++ L Sbjct: 171 VVTPQGELWDGLRGLRKDNTGYDLRDLFIGAEGTLGIITAAVLKLHPQPAARVTALAALA 230 Query: 232 NISDAAGIVPKIIKSKAIP--TAIEFMERQTI-LFAEDFLGKKFPDSSSNAYILL--TFD 286 + A + + +S A P T E M + L F ++P + +A I+L D Sbjct: 231 SPHAALDFL-SLTQSVAGPLLTGFELMSDFCLRLVGRHFEQMRYPFAEPHAQIVLLELSD 289 Query: 287 GNTKEQVEAEYETVANLCLAEG-AKDVYIVDTVERKDSVWSARGAFLEAIKASTTEMDEC 345 ++E A +E + L +G +D + +++ + + W+ R + +A + Sbjct: 290 SESEEHARALFERLMEQALEDGMVQDAVVAESLAQSRAFWNLR-EHIPLAQAEEGLNIKH 348 Query: 346 DVVVPRNRIAEFIEFTHDLAKEM---DVRIPSFGHAGDGNLHIYVCRDELCQADWEAKLA 402 D+ VP +RI FIE T D A E R+ +FGH GDGNLH V E D +A L Sbjct: 349 DIAVPISRIGHFIEET-DAAIEQAAPGARMVTFGHLGDGNLHYNVQAPE--GVDAKAFLE 405 Query: 403 EAMDR----MYAKALTFEGLVSGEHGIGYAKRKYLLNDFGTEHLALMAGIKQTFDPKNLL 458 + +Y G +S EHG+G K ++ + LM +K+ DP NL+ Sbjct: 406 QYQSPINRVVYDSVHRHRGSISAEHGLGQLKIDEAMHYKPDVEVQLMQAVKRALDPLNLM 465 Query: 459 NPKKV 463 NP KV Sbjct: 466 NPGKV 470 Lambda K H 0.318 0.136 0.388 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: 438 Number of extensions: 22 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: 466 Length of database: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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: 51 (24.3 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