Align 2-oxoacid:ferredoxin oxidoreductase 1, subunit alpha; OFOR1; EC 1.2.7.11 (characterized)
to candidate WP_084275835.1 B8779_RS07090 2-oxoglutarate synthase subunit alpha
Query= SwissProt::Q9YA13 (639 letters) >NCBI__GCF_900176045.1:WP_084275835.1 Length = 382 Score = 185 bits (470), Expect = 3e-51 Identities = 126/390 (32%), Positives = 198/390 (50%), Gaps = 31/390 (7%) Query: 243 VVASGNDVVAMGKVVGGVRYQAYYPITPASDE----SVLLEEFEGLKIDGESLGSIAILQ 298 V++SGN++ A + G R+ YPITP+S+ SVLL G +Q Sbjct: 5 VISSGNELAAKAAIDAGCRFFGGYPITPSSEVAHEMSVLLPRVGG-----------KFIQ 53 Query: 299 TEDEIAAVSSVIGAALTGARASTATSGPGFSLMVEALGWAGKNDVPMVITYYQRGGPSTG 358 EDEI ++ +GA+++G ++ T TSGPG SL E +G + P+VIT RGGPSTG Sbjct: 54 MEDEIGGIAVALGASMSGVKSMTNTSGPGISLKAEQIGLGFMTETPLVITNVMRGGPSTG 113 Query: 359 LPTRGSQSDLLFSLFASHGEFPRIILSSGDHLEAFYDAIEAYNLAERFQMPVIHLLDKFL 418 LPTR Q D+ + +HG++ I G E + + + A+N+AE PV LLD+ L Sbjct: 114 LPTRVQQGDINQAKAPTHGDYKSITFCPGSLEECYTEVVRAFNVAEELMTPVFVLLDETL 173 Query: 419 ANMVASVPFPDWKAIK---IDRGKTLFKAPTGPFKRF--PRDQPLADRPVLGSGAITWYT 473 +M PD + ++ +DR K P FK F P+D+P A P + G T Sbjct: 174 GHMHGKAVLPDLEEVQASIVDRAKPDPSIPKEEFKPFDVPQDKP-AVIPPMFQGYRFHLT 232 Query: 474 GDENDEYGHIDEDPVNRLVMYERRWKKMEIADREIPEDFRVKYYGDEDAEVLLVGWGSVK 533 G + G ED + ER +K+++ +++ + + + Y +DAE L+V +GSV Sbjct: 233 GLHHGPTGFPTEDAEICQNLIERLHRKIDVRRKDLLDSY--EEYMLDDAEWLIVAYGSVS 290 Query: 534 IPALEAIERLREMGVNAAYLHLRMLSPLPKRRVSEVLSRFDADRVIAVEAN---YLGQAS 590 A EAI RLR+ GV L P P+ ++ E+ RF A++++ E N Y+ + Sbjct: 291 RSAREAINRLRDQGVKIGMFRPITLWPSPEEKMKEIGERFPAEKILMPELNMGQYIDEVE 350 Query: 591 KIVTMETGFMFRKYILKWTGRPVYLHELVE 620 +++ + K GRP+ E++E Sbjct: 351 RVMKKRP-----VALNKANGRPISPAEIIE 375 Lambda K H 0.320 0.138 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: 569 Number of extensions: 23 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 639 Length of database: 382 Length adjustment: 34 Effective length of query: 605 Effective length of database: 348 Effective search space: 210540 Effective search space used: 210540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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