Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate H281DRAFT_04922 H281DRAFT_04922 iron complex transport system permease protein
Query= CharProtDB::CH_004160 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_04922 Length = 663 Score = 130 bits (327), Expect = 9e-35 Identities = 94/305 (30%), Positives = 154/305 (50%), Gaps = 23/305 (7%) Query: 25 VIPVPWRALLTDWQ-AGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASP 83 VI + + + WQ +H+ + +R+PRL +L G +A+AG ++Q + NP+ASP Sbjct: 369 VISLCFSVTMQGWQWTDAQHWSDVWFWRVPRLTASLGAGVMVALAGTILQRVTGNPMASP 428 Query: 84 DILGVNHAASLASVGALLLM--PSLPVMVLPLLAFAGGMAGLILLKMLAKTH--QPMKLA 139 D+LGV+ A L + A ++ PS PV++ + AG + L+ + L + P + Sbjct: 429 DLLGVSGGAMLGMLVAAVVATEPSTPVLLAG--SAAGALVCLLTIVTLGRRSGFAPEHVL 486 Query: 140 LTGVALSA--------CWASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMI 191 L G+A+SA AS Y L RP + L + + + + + + Sbjct: 487 LAGIAISAFAQAVIMLATASGGAYANLLRPLQYGSTYLIVPATA-------IAVGVCTVA 539 Query: 192 LFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGL 251 L L R L++L LG A LGV R L +A +T+ GP+SF+GL Sbjct: 540 AVLVAYLG-ARWLEILPLGANVADALGVGAQRARLLLLAVAAILTAGATVVIGPMSFVGL 598 Query: 252 VVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFV 311 + PH+ R + R R + V+AL G LL+V++D L R + P ++P GV+ ++G P+ + Sbjct: 599 MAPHLARLLGFPRARSQMLVAALIGGLLMVLSDWLGRNMIFPQQMPAGVIATLLGGPYLM 658 Query: 312 WLLVR 316 WLL R Sbjct: 659 WLLRR 663 Score = 125 bits (315), Expect = 2e-33 Identities = 91/272 (33%), Positives = 143/272 (52%), Gaps = 8/272 (2%) Query: 52 LPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVL 111 LPR+ +AL GAAL++AGV+ Q ++RNPLA P LGV+ A LA A ++ P+L + Sbjct: 65 LPRVAIALIAGAALSLAGVVFQQVLRNPLAEPLTLGVSAGAYLALTIAAVVAPALVADMR 124 Query: 112 PLLAFAGGMAGLILLKMLAKTHQP----MKLALTGVALSACWASLTDYLMLSRPQDVNNA 167 +A G A L +L +A T + + + L G+ ++ +L+ L + + + + Sbjct: 125 FTVALTG--AALAMLATMAMTWRKGFAAVSIVLAGMIVNLYCGALSVLLTIVFERSLTSV 182 Query: 168 LLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFW 227 +W GSL W+ V +P ++ + R L L +L D A+ LG+S+ TR Sbjct: 183 FIWGGGSLVQNGWAGVVWLLPRVLACGAAAALLVRPLTLFSLDDGSASQLGMSLAWTRPV 242 Query: 228 ALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLA 287 AL +AV +++ +A G I FIGL P + R + R R L + L GALLL +AD Sbjct: 243 ALAIAVILSAFVASAVGVIGFIGLGGPVLARLMGARRLRDQLLWAPLVGALLLAIADQAV 302 Query: 288 RIIHPPLE--LPVGVLTAIIGAPWFVWLLVRM 317 + + L LP G A+ G P +W+L R+ Sbjct: 303 QSLPGVLGELLPTGAAVALCGGPLLLWMLRRL 334 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: 580 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 318 Length of database: 663 Length adjustment: 33 Effective length of query: 285 Effective length of database: 630 Effective search space: 179550 Effective search space used: 179550 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: 51 (24.3 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