Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate GFF1141 Psest_1174 Hemoglobin-like flavoprotein
Query= CharProtDB::CH_003330 (396 letters) >FitnessBrowser__psRCH2:GFF1141 Length = 392 Score = 267 bits (683), Expect = 3e-76 Identities = 166/406 (40%), Positives = 229/406 (56%), Gaps = 25/406 (6%) Query: 1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA 60 ML A+ IA +KAT+PLL G LT HFY + + +PE++ +FN ++Q +G+Q AL N Sbjct: 1 MLCAEQIALIKATVPLLESGGEALTNHFYKLLLSEHPEVQPLFNQAHQASGEQPRALANG 60 Query: 61 IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPGQE----- 115 + YA +I+ L AL P V +I KH + Q+ PE Y +VG LL + E+ G+E Sbjct: 61 VLMYARHIDRLEALGPLVAQIINKHVALQVLPEHYPLVGSCLLRAIREVL--GEEIATDA 118 Query: 116 VLDAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPV 175 V+DAWG AY LA++ I +E ++Y A GGW G R FRI K S I SF L+P Sbjct: 119 VIDAWGAAYQQLADILIGQEEQLYQSKAEAVGGWRGARRFRIARKVVESDEIISFHLQPE 178 Query: 176 DGGAVAEYRPGQYLGVWLKPEGFPHQEIRQ-YSLTRKPDGKGYRIAVKREEGGQVSNWLH 234 DGG + ++ PGQY+G+ L+ +G +E+R+ YSL+ +G+ YRI+VKRE GG VSN LH Sbjct: 179 DGGPLMDFVPGQYIGLRLEIDG---KEVRRNYSLSAASNGREYRISVKREPGGVVSNALH 235 Query: 235 NHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLD-TLAKAGHTAQVNWF 293 + G ++L APAG+F + D P+ LIS GVG TP LAML+ LA A V++ Sbjct: 236 DMPK-GATLELFAPAGEFTLQ-PGDKPLVLISGGVGITPTLAMLEQALASA---RPVHFI 290 Query: 294 HAAENGDVHAF---ADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEG 350 H A N VHAF D + E L RF + + + A A G+ L E Sbjct: 291 HCARNAGVHAFRRSVDALAERHAQLKRFYCYEEHSNTASAPDAVGRLSERQL-----AEW 345 Query: 351 AFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL 396 +D + Y GP FM +QL LGV ++ YE FGP L Sbjct: 346 LPADRDVDAYFLGPKPFMAAVRRQLKALGVPEQQTRYEFFGPASAL 391 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: 377 Number of extensions: 20 Number of successful extensions: 7 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: 392 Length adjustment: 31 Effective length of query: 365 Effective length of database: 361 Effective search space: 131765 Effective search space used: 131765 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