Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Synpcc7942_0279 Synpcc7942_0279 NADH dehydrogenase (quinone)
Query= uniprot:Q39TW5 (635 letters) >FitnessBrowser__SynE:Synpcc7942_0279 Length = 534 Score = 473 bits (1217), Expect = e-138 Identities = 237/525 (45%), Positives = 333/525 (63%), Gaps = 17/525 (3%) Query: 31 CAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGICYLKV 90 C GC A+GA V A + + L GC G C GP+V P Y + Sbjct: 25 CTATGCRANGAEAVFKAVQQTIADQNLGDRCEAVSVGCLGLCGAGPLVQCDPSDRLYSDI 84 Query: 91 KPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRLDSKS 150 +P+ ++V+ + A + ++ PF+ Q + + + ++ Sbjct: 85 RPDQAADLVAAA------------QGAAMDLPEVDQAQ-PFFSQQLKIVNRHSGLINPDR 131 Query: 151 MDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKY 210 ++ YLA GGY AL +F +TP +V+ I+ S LRGRGGGG+P KW P K+ Sbjct: 132 LESYLAAGGYRALMHTIFDLTPTEVVEIIRLSGLRGRGGGGYPTGLKWATVAKMPSDRKF 191 Query: 211 VIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLA 270 V+ N DEGDPGAFMDR+++E +PH ++EG+ I AYAVGA+ G++YVR EYPLA+ +N A Sbjct: 192 VVCNGDEGDPGAFMDRSVLESDPHQVIEGMAIAAYAVGANFGYLYVRAEYPLAIARLNQA 251 Query: 271 IRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAV 330 IRQA RG +G +L S F F ++V +GAGAFVCGE +AL+ +++G G PR + + A Sbjct: 252 IRQARRRGLLGNSVLDSRFSFDLEVRIGAGAFVCGEETALIHSIQGERGVPRVRPPYPAE 311 Query: 331 KGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPM 390 G+W HP+++NNVET+AN+ I+ +GADWF + GT S GTK+F+L GK+ N GL+EVPM Sbjct: 312 SGLWGHPTLINNVETFANIAPIVEQGADWFAAIGTPTSKGTKVFALTGKLRNNGLIEVPM 371 Query: 391 GVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGM 450 G+ LR I+ G GIP KAVQTGGPSGGCIP A LD PVD+D L + GSMMGSGGM Sbjct: 372 GIPLRSIVD--GMGIP-ESPVKAVQTGGPSGGCIPLAQLDTPVDYDSLIQLGSMMGSGGM 428 Query: 451 IVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIELLEE 510 +VMDE+T MV IAR++++F + ESCGKC PCR G Q+ +L +++ G+G D++ LE+ Sbjct: 429 VVMDENTDMVAIARFYMEFCRSESCGKCIPCRAGTVQLHELLGKLSSGQGTAIDLQQLED 488 Query: 511 LAEST-GAALCALGKSAPNPVLSTIRYFRDEYEAHIREKKCPALS 554 L +LC LG SAPNP+LST+R+FR EYE+ + ++ AL+ Sbjct: 489 LCYLVKDTSLCGLGMSAPNPILSTLRWFRQEYESRLIPERAIALT 533 Lambda K H 0.319 0.138 0.420 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: 971 Number of extensions: 50 Number of successful extensions: 4 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: 635 Length of database: 534 Length adjustment: 36 Effective length of query: 599 Effective length of database: 498 Effective search space: 298302 Effective search space used: 298302 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 (21.7 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