Align Uncharacterized protein (characterized, see rationale)
to candidate HSERO_RS19090 HSERO_RS19090 C4-dicarboxylate ABC transporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >FitnessBrowser__HerbieS:HSERO_RS19090 Length = 431 Score = 447 bits (1149), Expect = e-130 Identities = 236/408 (57%), Positives = 306/408 (75%), Gaps = 7/408 (1%) Query: 10 IFIAMLLGVLAGTAAHHYAPDPAAAKSIADHLSILTDVFLRMIKMIIGPLVFATLVSGIA 69 IF AMLLG+L G + D A AK +A ++SI +D+FLR+IKM+I PLVF+TLV GIA Sbjct: 11 IFAAMLLGILVGYLIFSHN-DKAQAKELAGYISIASDLFLRLIKMVIAPLVFSTLVVGIA 69 Query: 70 SMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLALPAADAA-SNLKTG 128 MGD K+VGRI K++AWF AS+ SL LG++MANLL+PG G+ ALP+ DAA + L T Sbjct: 70 HMGDAKSVGRIFGKSLAWFFIASLVSLALGMIMANLLQPGAGV--ALPSPDAAGAGLATS 127 Query: 129 ALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIGKPVLAGIEGLSHV 188 ++EF H+ PKS VEAMA NE+LQ+VVFS+FFG AL +L + GK +LA I+ LSH Sbjct: 128 KFTVKEFFNHLVPKSIVEAMAQNEVLQVVVFSMFFGIALASLGER-GKHLLAVIDDLSHT 186 Query: 189 MLKITNYVMAFAPVGVFGAVAAVITAEGLGVLVVYAKLLGAVYLSLALLWVALIAGGYFF 248 MLKIT YVM FAPV VF A+AA + GL +LV +A + Y SL LLWV LIA G+ F Sbjct: 187 MLKITVYVMKFAPVAVFAAMAATVAVNGLEILVSFAVFMRDFYFSLVLLWVILIAVGFIF 246 Query: 249 LGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITGFVLPLGYSFNLDG 308 L + +F LL +++ ++ FATASSE+AYPK+++ L RFGVK +I+ FV+P+GYSFNLDG Sbjct: 247 LKKRIFHLLALIKEAFLLAFATASSEAAYPKLLDALDRFGVKRKISSFVMPMGYSFNLDG 306 Query: 309 SIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASLVVVAAVLPMFGLP 368 S++Y +FA LF+AQ YGIH+ +S Q+TM+LVL++TSKGIAGVPRASLVV+AA L F +P Sbjct: 307 SMIYCTFATLFIAQAYGIHMPISTQITMMLVLMLTSKGIAGVPRASLVVIAATLHQFNIP 366 Query: 369 EAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSEGAIGAPVPEEA 416 EAG+L++LGID LDMGR+ TN +GN+IA+ VVAK EG G EEA Sbjct: 367 EAGLLVILGIDTFLDMGRSATNAVGNSIASAVVAKWEG--GLMTEEEA 412 Lambda K H 0.325 0.141 0.401 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: 448 Number of extensions: 21 Number of successful extensions: 4 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: 436 Length of database: 431 Length adjustment: 32 Effective length of query: 404 Effective length of database: 399 Effective search space: 161196 Effective search space used: 161196 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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