Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate GFF3846 PGA1_78p00100 flavohemoprotein Hmp
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Phaeo:GFF3846 Length = 396 Score = 274 bits (700), Expect = 4e-78 Identities = 165/398 (41%), Positives = 227/398 (57%), Gaps = 20/398 (5%) Query: 2 LDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQR-NGDQREALFNA 60 L Q+ A V AT+P L G + A Y R+ + ++K +FN S+Q+ + Q AL NA Sbjct: 5 LSEQSKAIVTATVPALEAHGGAIVAEMYTRLLA-DEDIKALFNQSHQQGDSSQHAALANA 63 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMF--SPGQEVLD 118 I YA NI+NL AL VE+I KH S QIKPE Y V LL ++ + + EVL+ Sbjct: 64 ILGYARNIDNLGALSSVVERIVNKHVSLQIKPEHYTHVATALLGAIEAVLGQAASPEVLE 123 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AWG+AY LAN+ I E ++Y++ A+ GGW G R+F IV SA + SF L PVDGG Sbjct: 124 AWGEAYWFLANLLIEAERKMYDDIANAEGGWNGWREFVIVGIIGESASVKSFVLRPVDGG 183 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEI----RQYSLTRKPDGKGYRIAVKREEGGQVSNWLH 234 V ++PGQYL F H + R YS++ P+G+ YRI+VKRE GG +S WLH Sbjct: 184 PVLRHQPGQYLAF-----DFDHPDTGKARRNYSISCAPNGEYYRISVKREPGGVISGWLH 238 Query: 235 NHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFH 294 A G V+++ APAGDF + + V L+SAGVG TPM+AML+TLA +A + H Sbjct: 239 EVATEGTVLRVAAPAGDFVLKDRPEGEVVLLSAGVGLTPMVAMLETLAANDRSA--TYLH 296 Query: 295 AAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSD 354 AA +GD A ++ L +SL + + + PS+ADRA ++D EG + L + Sbjct: 297 AAVDGDNLA----MEGLSKSLAKRSV-IFLETPSDADRAAARYDVEGRITPDWLAANTNT 351 Query: 355 PTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 +Y+CGP GFM L V + IH+E FGP Sbjct: 352 ALSDYYICGPKGFMAMAIAGLRAANVDMDRIHFEFFGP 389 Lambda K H 0.318 0.135 0.404 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: 403 Number of extensions: 21 Number of successful extensions: 5 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: 396 Length of database: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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: 50 (23.9 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