Align indolepyruvate ferredoxin oxidoreductase (subunit 2/2) (EC 1.2.7.8) (characterized)
to candidate WP_011385598.1 AMB_RS16325 4Fe-4S dicluster domain-containing protein
Query= BRENDA::Q6LZB6 (578 letters) >NCBI__GCF_000009985.1:WP_011385598.1 Length = 618 Score = 488 bits (1255), Expect = e-142 Identities = 269/598 (44%), Positives = 384/598 (64%), Gaps = 29/598 (4%) Query: 4 LMLGNEAVARGAYEAGVLVATAYPGTPSTEITEHISKYPEINSEWSVNEKVALEVAIGSA 63 L+ GN+A+ARG +EAG VA AYPGTPSTEI E +S YP++ +EWSVNEKVA+EVAIG + Sbjct: 14 LLSGNDAIARGVWEAGAKVAAAYPGTPSTEILESLSLYPDLYAEWSVNEKVAMEVAIGGS 73 Query: 64 IAGARTVVSMKHVGLNVAADPLMTVAYTGINAGLLIIVADDPSMHSSQNEQDTRYYGIFS 123 ++GAR+ +MKHVGLNVA+D MTV G+ GL+I VADD M SSQNEQD+R++G F+ Sbjct: 74 MSGARSFCAMKHVGLNVASDAFMTVTVAGVIGGLVIAVADDVGMSSSQNEQDSRFWGRFA 133 Query: 124 KIPVLEPSDSQECKDFVKLGLEISEKFDTPVILRLSTRVSHSQSLVELEEKEKIELKPYD 183 +PVLEP+DSQE + K E+SE ++TPVILRL+TRV H +++V++ EK ++ + Sbjct: 134 HVPVLEPADSQEAYEMAKYAFELSEAYNTPVILRLTTRVCHVKAVVQVGEKVAHDIGGFK 193 Query: 184 YNPSKYVSAPANAKKRRIFIEERLKELSNFADSSDVNKIEYA-NKKIGIITSGVAYNYAK 242 + ++V PANAK R +L A++S +N ++ +K++G +TSG AY + + Sbjct: 194 SDARRWVMTPANAKGLLPAQIAREGKLQALAEASPMNFLDDGPDKRVGFVTSGPAYMHVR 253 Query: 243 EAVSDASFLKFGMSYPLPEEKIKEFVQNCDKVYVFEELEPIFEQKIRSMGLNVI-GKEIF 301 E+ DA LK G +YP+P +++ + + V EE EP+ EQ++++ GL I GK++ Sbjct: 254 ESFPDAPVLKLGFTYPVPVALVEKLAAQVEHLVVVEETEPLMEQELKAAGLQAIHGKDLL 313 Query: 302 PIVGELSSEIIRNAL---LNE---SKIVIEKIEDLPQRPPVLCPGCHHRGPFYVLKKLK- 354 P +GEL+ ++ A+ L E K + P RPP +C C H G +Y L +++ Sbjct: 314 PRLGELTPNVLIPAIKTFLGEPLPPTTTYPKFDPFP-RPPTMCAACPHMGVYYSLARMRK 372 Query: 355 -LHVAGDIGCYTLGGFEPLNAIDTTICMGASIGMAHGFEMARGKEFAKKS-VAVIGDSTF 412 + ++GDIGCYTLG P NA+D+TI MGAS+G+A G + AR +E K+ VAVIGDSTF Sbjct: 373 NVQISGDIGCYTLGAGHPWNALDSTISMGASMGIALGMDKARTEETKDKAVVAVIGDSTF 432 Query: 413 WHSGVTGLIDIVYNKGHSTVIILDNSITAMTGHQENPSTGKTLSGERTNQIDFEALGRSI 472 H G+ GL+DIVYN+G+ TV+ILDN T MTG Q + TGK L G+ T ++DF L ++ Sbjct: 433 LHMGMQGLLDIVYNRGNVTVLILDNRTTGMTGGQNHAGTGKGLKGDDTPRVDFAKLVEAL 492 Query: 473 GI--NRICVVDAYDLKALEETIKEEVNAEEPSLIITKRPCVLIKGAKFDFKDYKIDPKLC 530 G+ RI +D Y L + +TIK+E E S+IIT RPCVL + + YK+ + C Sbjct: 493 GVKPERISKIDPYVLPVVFKTIKQETAIPEVSVIITDRPCVLSE-FYTKIEPYKVIDEDC 551 Query: 531 TGCKLCLKAGCPAISF---------DGKV-----AKINDSLCVGCGLCKDLCKFSAIV 574 TGC C+ GCPAI+ DGKV I+ ++C GC +C + C AIV Sbjct: 552 TGCGNCINVGCPAITVKRSESKVRPDGKVNELKFTTIDTAMCTGCHMCVESCGPKAIV 609 Lambda K H 0.317 0.136 0.392 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: 871 Number of extensions: 42 Number of successful extensions: 11 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: 578 Length of database: 618 Length adjustment: 37 Effective length of query: 541 Effective length of database: 581 Effective search space: 314321 Effective search space used: 314321 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: 53 (25.0 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