Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate PfGW456L13_3769 Hemin ABC transporter, permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3769 Length = 345 Score = 172 bits (436), Expect = 1e-47 Identities = 123/337 (36%), Positives = 184/337 (54%), Gaps = 27/337 (8%) Query: 6 VIFITLALAGCALLSLHMGVIPVPWRALLT----------DWQAGHEHYYVLMEYRLPRL 55 +IF+ L L LSL +G + +P L D + +L + RLPR Sbjct: 11 LIFLLLLLVLVFWLSLALGPVSLPLGDTLLGGMRLLGLPLDGGDTQQAELILGQIRLPRS 70 Query: 56 LLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALL---LMPSLPVMVLP 112 LL + VG+ LA++GV +QG+ RNPLA P ++GV+ A+L + A++ L+ LP ++ P Sbjct: 71 LLGIAVGSVLALSGVAMQGLFRNPLADPGLVGVSGGAALGAALAIVGGSLLGGLPPVIEP 130 Query: 113 LL----AFAGGMAGLILLKMLAKTHQPMKLA---LTGVALSA-CWASLTDYLMLSRPQDV 164 L AFAGG+ ++ + + +A L GVA++A A + + L+ + Sbjct: 131 YLLSVCAFAGGLIVTAVVYRFGRRNGQTDVATMLLAGVAMTAMAGAGVGLFTYLADDATL 190 Query: 165 NNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRD---LDLLALGDARATTLGVSV 221 W GSL G + + PL+I+ L ++L R L+ L LG++ A LG + Sbjct: 191 RTLTFWNLGSLNGASYPRLW---PLLIVTLGVALWLPRRAAALNALLLGESEARHLGFDI 247 Query: 222 PHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLV 281 + +L VAA G I FIGLVVPH+MR + G HR LLP S L GA LL+ Sbjct: 248 ERIKLELVLCTALGVGAAVAAAGLIGFIGLVVPHLMRLLVGPDHRVLLPASLLAGASLLL 307 Query: 282 VADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318 +ADL AR++ P ELP+G++TA+IGAP+F++LLVR R Sbjct: 308 LADLAARLLLAPAELPIGIVTALIGAPFFLYLLVRGR 344 Lambda K H 0.330 0.142 0.447 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: 304 Number of extensions: 15 Number of successful extensions: 2 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: 318 Length of database: 345 Length adjustment: 28 Effective length of query: 290 Effective length of database: 317 Effective search space: 91930 Effective search space used: 91930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 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