Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate RR42_RS09175 RR42_RS09175 flavohemoprotein
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS09175 Length = 403 Score = 256 bits (655), Expect = 6e-73 Identities = 157/401 (39%), Positives = 219/401 (54%), Gaps = 14/401 (3%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML Q+ + A++P+L E G +T FY MF PEL +FNM NQ NG Q+++L +A Sbjct: 1 MLSEQSRPLIDASVPVLREHGLAITQTFYRNMFADRPELTNLFNMGNQANGSQQQSLASA 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118 + AYA+N + AL P V +I KH S IKP Y IV HLL + E+ ++ Sbjct: 61 VFAYAANYGDNSALAPVVSRIVHKHASVGIKPSHYAIVARHLLGAIGEVLGDAATPALVA 120 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AW +AY +LA I EA +Y A G + + RIVA+ +SA IT+F LE V G Sbjct: 121 AWDEAYWLLAAELIAAEARLY---AHAQTGPDHRQPVRIVAREEQSADITAFTLEAVGGT 177 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG-------GQVSN 231 +A++ PGQY+ V ++ Q+ RQYSL+ P+GK +RI+VKRE G G VSN Sbjct: 178 TLADFLPGQYISVVVELTPGTFQQ-RQYSLSDAPNGKTWRISVKRERGNGEDLPAGTVSN 236 Query: 232 WLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVN 291 WLH +A GDV+ + P GDF + TP+ L+SAGVG TPM++ L+T+A+ + +V Sbjct: 237 WLHENAREGDVLLVSQPFGDFAPRIEPSTPIVLLSAGVGVTPMISALNTVAQRNPSRKVV 296 Query: 292 WFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGA 351 + HAA A +VK + LP H ++ + E Q G MD+ + Sbjct: 297 FGHAARMVSHVAHLKDVKHAARKLPELRTH-FFLESEEPAEFLAQPALPGRMDIDVILAN 355 Query: 352 FSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 FYLCGP+ FMQ L GVK + +H E FGP Sbjct: 356 EDLADADFYLCGPLPFMQAQRAALQARGVKADRVHREVFGP 396 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: 435 Number of extensions: 20 Number of successful extensions: 6 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: 403 Length adjustment: 31 Effective length of query: 365 Effective length of database: 372 Effective search space: 135780 Effective search space used: 135780 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