Align Putative L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF (characterized, see rationale)
to candidate YP_426500.1 Rru_A1412 4Fe-4S ferredoxin
Query= uniprot:A0A0C4Y8G6 (489 letters) >NCBI__GCF_000013085.1:YP_426500.1 Length = 484 Score = 518 bits (1335), Expect = e-151 Identities = 280/485 (57%), Positives = 331/485 (68%), Gaps = 11/485 (2%) Query: 8 QDSAAPLHFVPAADFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLG 67 QD+AA P A F ++R AL+DP+LR++FR AMD L +KRA QF D DE LR G Sbjct: 7 QDTAAT---APLA-FTGKARVALNDPRLRANFRRAMDGLMSKRAAQFADADEWRTLRARG 62 Query: 68 EAIRQHALSQLPDLLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSM 127 R AL++LPDLL +LE + + VHWAET +ANAIV + A A VIKGKSM Sbjct: 63 AEARARALAKLPDLLERLERRCAENAITVHWAETTGQANAIVLDLLTAAGAKTVIKGKSM 122 Query: 128 ASEEIELNHYLAERGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPG 187 SEE+ LN +LA GI IESD+GEYI+QLAGE PSHIVMP IHK + +IA LF +HIPG Sbjct: 123 VSEEMHLNAHLAAHGITAIESDLGEYIIQLAGEAPSHIVMPCIHKNKAEIAALFAEHIPG 182 Query: 188 TPYTEDVDELIQTGRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDV 247 PYTE+VD+L R ALR F AD G+SGVNFA A+TGTL L+ENEGNGRLSTT+P + Sbjct: 183 QPYTENVDDLTGAARNALRGAFAAADAGISGVNFAVAETGTLVLIENEGNGRLSTTLPPL 242 Query: 248 HIAIMGMEKVVARLEHIVPLASLLTRSATGQAITTYFNLISGPRRAGERDGPREVHLVLL 307 HIA+ G+EKV+ L+ + PL SLL RSATGQ ITTY N+ISGPRR GE+DGP+ VHLVLL Sbjct: 243 HIAVTGIEKVLEFLDDVPPLLSLLPRSATGQPITTYVNMISGPRRPGEKDGPQAVHLVLL 302 Query: 308 DNGRSQAYADEQLRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLD 367 DNGRS+ Y D QLR TL+CIRC AC+NHCPVYTR+GGH+Y TYPGPIGKI+SP L GLD Sbjct: 303 DNGRSRVYDDPQLRDTLRCIRCAACLNHCPVYTRVGGHSYSFTYPGPIGKILSPQLEGLD 362 Query: 368 ATADLATASSLCGACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEH 427 D ASSLCGAC EVCPV IPIP LL+RLR EA S V +G G+ S G+ Sbjct: 363 CAGDQPHASSLCGACAEVCPVEIPIPDLLVRLRGEAISPTSRAV----KGGGSARSLGDR 418 Query: 428 LVWRFWSGAFAHPLAYRLFRWAATRLRVLTPKHQLG---WTRHRAPLTPAPRSLSDLLRE 484 L R + P Y L A R+ P G WTR R+ A RSL L RE Sbjct: 419 LGRRLSTAILGQPRLYGLISRLAGRIGDRLPSWLPGLNRWTRVRSKPAFARRSLHALARE 478 Query: 485 RGQAE 489 RG A+ Sbjct: 479 RGYAD 483 Lambda K H 0.320 0.135 0.406 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: 652 Number of extensions: 26 Number of successful extensions: 3 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: 489 Length of database: 484 Length adjustment: 34 Effective length of query: 455 Effective length of database: 450 Effective search space: 204750 Effective search space used: 204750 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 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