Align aldehyde ferredoxin oxidoreductase (EC 1.2.7.5) (characterized)
to candidate WP_011383898.1 AMB_RS07515 aldehyde ferredoxin oxidoreductase
Query= BRENDA::Q51739 (605 letters) >NCBI__GCF_000009985.1:WP_011383898.1 Length = 569 Score = 209 bits (532), Expect = 3e-58 Identities = 188/575 (32%), Positives = 266/575 (46%), Gaps = 54/575 (9%) Query: 9 IRVNLSTGDI-KVEEYDEELAKKWLGSRGLAIYLLLKEMDPTVDPLSPENKLIIAAGPLT 67 + V+L++ I K E ++LA+ R L LL+ VDPL P+N LI +AGP Sbjct: 5 LHVDLTSRTITKAEIRGDDLAR---AGRYLIARTLLESGVARVDPLGPDNPLIFSAGPYA 61 Query: 68 GTSAPTGGRYNVVTKSPLTGFITMANSGGYFGAELKFAGYDAIVVEGKAEKPVYIYI-KD 126 GT+ R +V KSPLTG I AN+GG F L + + G ++ V I I K+ Sbjct: 62 GTNLSNANRLSVGCKSPLTGGIKEANTGGTFAVALGQLALAGLTLHGCCDEWVVIRITKE 121 Query: 127 EHIEIRDASHIWGKKVSETEATIRKEVGSEKVKIASIGPAGENL-----VKFAAIMNDGH 181 I A GK E A + + G +KV IA GP GE L + F+ Sbjct: 122 GDITFTSAEPYLGKGTFEVAAMLHEAYG-KKVSIAQCGPVGERLGLLGGISFSDREGRPA 180 Query: 182 RAAGRGGVGAVMGSKNLKAIAVEGSKTVPIADKQKFMLVVREKVNKLRNDPVAGGGLPKY 241 R A RGGVGAVMGSK +KAI V+ +K + D+ K M ++ KL ++ + + Sbjct: 181 RLAARGGVGAVMGSKKVKAIVVDLTKIPELHDRAKVMASTKDYAAKL-SEQAPVKAMKER 239 Query: 242 GTAVLVNIINENGLYPVKNFQTG--VYPYA--YEQSGEAMAAKYLVR-NKPCYACPIGCG 296 GTA++ + N G PV+NF G V P + G+ + + + R P +AC GC Sbjct: 240 GTAMVGDFTNYVGGMPVRNFSAGQLVDPKVEPLKVGGDYIRERNMGRGGNPSHACMPGCV 299 Query: 297 RVNRLPTVGE-----TEGPEYESVWALGANLGINDLASIIEANHMCDELGLDTISTGGTL 351 V E EYE++ LG N G++D I N++C++LG+DTI TG T+ Sbjct: 300 IQCSNEYVDENGKELVSPLEYETLGLLGTNCGLDDPDDIARLNYICNDLGIDTIETGATM 359 Query: 352 ATAMELYEKGHIKDEELGDAPPFRWGNTEVLHYYIEKIAKREGFGDKLAEGSYRLAESYG 411 ME A +G+ + + I G LA+G+ R+ E YG Sbjct: 360 GVLME--------------AGQGAFGDVGFVAQALADIGAGNERGRLLAQGTARVGEHYG 405 Query: 412 HPELSMTVKKLELPAYDPRGAEGHGLGYATNNRGGCHIKNYMISPEILGYPYKMDPHDVS 471 + + +KK + AYDPR E G+ T +G H G MD D S Sbjct: 406 VRRVPV-IKKQAISAYDPRVIEVTGVSMMTTAQGADH---------TTGNLPMMDTKDKS 455 Query: 472 -DDKIKMLILFQDLTALIDSAGLCLFTTFGLGADDYRDLL----NAALGWDFTTEDYLKI 526 + ++ I Q A+ DS GLC+F D R LL NA G E +L+I Sbjct: 456 VAEVVEASITAQINAAIADSLGLCVFGR--SVTDTNRQLLAEAVNACHGTSIDPEFFLEI 513 Query: 527 GERIWNAERLFNLKAGLDPARDDTLPKRFLEEPMP 561 G E FN +AG A DD LP+ FL+E +P Sbjct: 514 GRETLRLEHRFNQEAGFLTA-DDELPRFFLDEALP 547 Lambda K H 0.316 0.138 0.414 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: 865 Number of extensions: 46 Number of successful extensions: 7 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: 605 Length of database: 569 Length adjustment: 37 Effective length of query: 568 Effective length of database: 532 Effective search space: 302176 Effective search space used: 302176 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 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