Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_058857632.1 AS188_RS03230 hemin transporter
Query= CharProtDB::CH_003330 (396 letters) >NCBI__GCF_001482365.1:WP_058857632.1 Length = 400 Score = 215 bits (548), Expect = 2e-60 Identities = 143/402 (35%), Positives = 206/402 (51%), Gaps = 20/402 (4%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKE-IFNMSNQRNGDQREALFN 59 ML VKAT+P++ E ++ FY MF +PEL + +FN NQ +G Q++AL Sbjct: 1 MLSDTAYPVVKATLPVVGENIQEIAKRFYAHMFAEHPELLDGLFNRGNQADGRQQQALAG 60 Query: 60 AIAAYASNIENLPALLP--AVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QE 115 ++A YA + N P LP + +IA KH S + PEQY IV HL+ + ++ +E Sbjct: 61 SVAGYAGYLVNKPTELPDHLLSRIAHKHVSLGLAPEQYQIVHNHLMWAIVDVLGEAVTEE 120 Query: 116 VLDAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPV 175 V AW + Y ++AN I +E +Y A++ R +R+V K +A + +F +E V Sbjct: 121 VAAAWDEVYWLMANALITQERGLYE--ATRLSPDTVWRTWRVVEKITETADVVTFVVERV 178 Query: 176 DGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEG-----GQVS 230 D V PGQY+ ++ HQ RQYSLT+ DG+ AVKR G G++S Sbjct: 179 DEREVKPSLPGQYVTCKMEMPDGVHQP-RQYSLTKADDGRHRVFAVKRIRGNGTPAGEMS 237 Query: 231 NWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQV 290 LH+ +GD + L AP GD + D PV L+SAG+G TPM ML L G +V Sbjct: 238 TLLHDQVQIGDEITLSAPFGDVVLEYTD-RPVVLVSAGIGITPMAGMLSHLVAGGAQRKV 296 Query: 291 NWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEG 350 HA + + A +V + L + W+ PS A G + GLMD+ +E Sbjct: 297 LLLHADASPESFALRAQVTADLEELLDGSLAVWFEHPSPAP---GPNEHAGLMDVRAVE- 352 Query: 351 AFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392 Q+YLCGP+ FMQ L+ GV ++I YE FGP Sbjct: 353 --LPAQAQYYLCGPLPFMQAVRSDLIARGVPAKDIQYEVFGP 392 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: 439 Number of extensions: 24 Number of successful extensions: 9 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: 400 Length adjustment: 31 Effective length of query: 365 Effective length of database: 369 Effective search space: 134685 Effective search space used: 134685 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