Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_012335291.1 M446_RS27110 NO-inducible flavohemoprotein
Query= CharProtDB::CH_003330 (396 letters) >NCBI__GCF_000019365.1:WP_012335291.1 Length = 403 Score = 310 bits (795), Expect = 4e-89 Identities = 168/394 (42%), Positives = 227/394 (57%), Gaps = 5/394 (1%) Query: 2 LDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQ-RNGDQREALFNA 60 L TI VKAT+P L + G +T Y+RMF NP+++++FN S+ G Q +AL A Sbjct: 5 LSDATIHLVKATVPALQQHGLAITRRMYERMF-QNPDIRDLFNQSHHGETGSQPKALAQA 63 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118 + AYA NI+NL AL PAVE+IAQKH I P+ Y V E LL + ++ E+L Sbjct: 64 VLAYAQNIDNLGALAPAVERIAQKHVGLTILPDHYPHVAEALLGAIKDVLGGAATDEILA 123 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AWG+AY LA+V I RE IY A+ GGW G R+F+I ++ S +ITSF L P DGG Sbjct: 124 AWGEAYWFLAHVLIGRETAIYTSLAAAPGGWRGWRNFKIDSRRRESEIITSFILRPEDGG 183 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNWLHNHAN 238 V ++PGQYL W+ G H R YS++ P + YRI+VKRE G SNWLH+ A Sbjct: 184 RVLRHQPGQYLTFWIDIPG-QHPLKRNYSISSAPSEEAYRISVKREPNGIASNWLHDQAQ 242 Query: 239 VGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAAEN 298 G ++++ PAG+FF+ PV L+S GVG TPM++ML+T+A QV + H N Sbjct: 243 EGQILRVAPPAGEFFLNEESPRPVVLLSGGVGLTPMMSMLETIASQHPNVQVQYVHGTLN 302 Query: 299 GDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDPTMQ 358 G HA + V L Q+ TA T+Y +P DR +D GL+ + L+ Sbjct: 303 GSTHAMKEHVASLTQAHGNITATTFYVEPRAEDRQGQDYDHAGLISVDWLQANTPLGEAD 362 Query: 359 FYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 FYLCGP F++ L GV+ + IHYE FGP Sbjct: 363 FYLCGPRPFLRAFVSGLALAGVRSDRIHYEFFGP 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: 421 Number of extensions: 23 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: 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 24 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