Align 2-oxoacid oxidoreductase (ferredoxin) (subunit 2/2) (EC 1.2.7.11) (characterized)
to candidate WP_083763501.1 AMB_RS10840 2-oxoacid:acceptor oxidoreductase subunit alpha
Query= BRENDA::Q4J6I9 (621 letters) >NCBI__GCF_000009985.1:WP_083763501.1 Length = 565 Score = 224 bits (570), Expect = 1e-62 Identities = 175/579 (30%), Positives = 272/579 (46%), Gaps = 68/579 (11%) Query: 4 GPQGLGVDTSANVFSNAIARAGYYLFGNREYYSNIKGRHSYFEVVFDEKPVRSISSYTNI 63 G G GV T+AN+F +A A AGYY R I+G + V +P+ S+ +I Sbjct: 3 GSGGAGVMTAANMFLDAAAEAGYYALFGRSSGPQIRGGEAAALVRLGVEPITSVDDTFDI 62 Query: 64 LATFDAETLFQHFTEVTDFVIYGTDYATTNIDMVKSMEPEMAEQIKQLLSENKMGYTIKD 123 + D + + + E+ + + + +P + + D Sbjct: 63 MLAIDWQGVQRFAAELP-----------LSKNSIVICDPSAGD--------------VPD 97 Query: 124 VITYLKNKGIKVIELDYLDILKKIAAELKVQVSVVERAKNMAAVGASIGLLGLPFDILEN 183 V Y+K G K++ L D+ K+I NM A+GA L+G+P L Sbjct: 98 V--YVKT-GAKIVHLHMKDLAKEIPGG----------RPNMIALGAVAELIGIPVGPLTE 144 Query: 184 TISSIF---RNDLFVKMNVMAAKIGYNTVNNTYHLEVINNVKP----RIQIDGNTIAAMG 236 + R D + + +V K G + + K R + GN A +G Sbjct: 145 VLGKSLKKKRADAY-EASVAGVKAGAAAAATLGGAKRLAAAKAKDAKRWTVTGNYGAGLG 203 Query: 237 KIAGGLRFQSYYPITPASDESVYIEANQNVDMIVEGNELRKGGVVVVQAEDELAAINMAI 296 I GG+RF + YPITPA++ Y+ + L K G V VQAEDELA+INM + Sbjct: 204 AIRGGVRFCAAYPITPATEVLEYL-----------ASALPKVGGVFVQAEDELASINMCL 252 Query: 297 GAALTGARTSTATSGPGFSLMAEGLSWAGMNEVPVVVTYYMRGAPSTGLPTRSGQADLKF 356 GA+ G + T+T+GPG SLM EGL A +E PVVV R PSTG+ T+ Q+DL Sbjct: 253 GASYGGEASITSTAGPGLSLMTEGLGLAVASETPVVVVDVQRVGPSTGIATKCEQSDLNI 312 Query: 357 ALNAGHGEFPRIVIASGDHHEIFWDSIWALNLAERYQTPVIHIIEKALANAYSLIDEDSI 416 A+ HG+ P +V+A + + + W + LAE QT + + ++AL + ++ID + Sbjct: 313 AVYGLHGDAPHLVVAPNSVGDCIFTTQWGVYLAESLQTACLVMSDQALGQSRAIIDAPA- 371 Query: 417 KGQIKIDRGKLVKQV---GDRFNRFQPSDDGISPRVFLGQSSIFYTGD--EHNEEGHITE 471 + +LV + G+ F R+ + GISP GQ YT D EH E G + Sbjct: 372 --DVAFVGKRLVAEAPAEGEVFKRYANTASGISPMPVPGQPGCQYTSDGLEHTETGTPSS 429 Query: 472 NSLNRTKMHEKRMKKLETADNEIPEELRVNVVGDADIVLITWGSPKGAILDAMSELEKDG 531 S + T +KR +KL D + G+ DI +ITWGS GA +A++ + DG Sbjct: 430 QSSDHTLQLDKRQRKLTNFDY---GNHWATIEGEGDIAVITWGSCTGAAREAVARAKADG 486 Query: 532 IKTMMVQVKMFNPYPTKLVKKLLEGKSKIVAVENNYQAQ 570 I ++ +++ +P + + L+G SKI+ VE ++Q Q Sbjct: 487 INAKLISLRLISPIRPQHLADALKGVSKILVVEQSHQGQ 525 Lambda K H 0.316 0.134 0.377 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: 745 Number of extensions: 40 Number of successful extensions: 7 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: 621 Length of database: 565 Length adjustment: 37 Effective length of query: 584 Effective length of database: 528 Effective search space: 308352 Effective search space used: 308352 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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