Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate 7026032 Shewana3_3174 globin (RefSeq)
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__ANA3:7026032 Length = 397 Score = 412 bits (1059), Expect = e-120 Identities = 213/399 (53%), Positives = 267/399 (66%), Gaps = 5/399 (1%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 MLD++TI +K+TIPLL GP LT HFY+RMF HNPELK++FN+++Q +G Q ALFNA Sbjct: 1 MLDSRTIQVIKSTIPLLESAGPVLTQHFYERMFKHNPELKDVFNLAHQHSGGQPVALFNA 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPG--QEVLD 118 +AAYA NI+NL AL AVE+IA KHT F I+PEQY IVG HLLATL E+ +EVL Sbjct: 61 VAAYAKNIDNLGALGSAVERIAHKHTGFLIQPEQYAIVGSHLLATLKELGGKAVTEEVLT 120 Query: 119 AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG 178 AW AYG LAN+FINREA+IY E+A + GGW G R+F I K S I SF L PVDG Sbjct: 121 AWADAYGFLANIFINREAQIYQESAQQDGGWSGVREFIISEKKAESLEIASFVLTPVDGK 180 Query: 179 AVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNWLHNHAN 238 AV ++ PGQYL + + EIRQYSL+ P+G+ YRI VKRE GQVSN LH+ Sbjct: 181 AVKDFIPGQYLSIKAQHPKLAFDEIRQYSLSDAPNGQSYRITVKRELNGQVSNLLHDVLQ 240 Query: 239 VGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNWFHAAEN 298 VGD + ++ PAGDF +AV +TPV LISAGVGQTPM +ML+ L K H + V W HA E+ Sbjct: 241 VGDTLSVMPPAGDFTLAVQAETPVVLISAGVGQTPMKSMLNQLLKLRHPSTVTWLHACEH 300 Query: 299 GDVHAFADEVK-ELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAFSDPTM 357 G VH F +K +LGQ +H WYR+P++AD +D EG M+L+ + Sbjct: 301 GGVHGFKSAIKNKLGQH-ANLASHVWYREPTKADMLGQDYDFEGTMNLTSVADKIV-ANA 358 Query: 358 QFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 +Y CGP+GFM +QL+ GV E +HYE FGPH L Sbjct: 359 HYYFCGPIGFMASIKQQLLAFGVPSEQMHYEVFGPHAEL 397 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: 461 Number of extensions: 19 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 365 Effective length of database: 366 Effective search space: 133590 Effective search space used: 133590 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