Align Uncharacterized protein (characterized, see rationale)
to candidate BWI76_RS19175 BWI76_RS19175 dicarboxylate/amino acid:cation symporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >FitnessBrowser__Koxy:BWI76_RS19175 Length = 424 Score = 418 bits (1075), Expect = e-121 Identities = 206/416 (49%), Positives = 293/416 (70%), Gaps = 1/416 (0%) Query: 4 NRLPTLIFIAMLLGVLAGTAAHHYAPDPAAAKSIADHLSILTDVFLRMIKMIIGPLVFAT 63 N+L I I MLLG+L+G A H YA + ++++++LTDVFLR+IKM+I PLVF+T Sbjct: 5 NKLTLFIVIFMLLGILSGAAIHAYAGQTTIT-AWSENITLLTDVFLRLIKMVIAPLVFST 63 Query: 64 LVSGIASMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLALPAADAAS 123 L GI +G+ +GR+G KAM WFI +SI S+L+GL++ L PG G+NLA+P + Sbjct: 64 LTVGIMRLGETATIGRVGGKAMVWFITSSILSILVGLVIVTLEHPGAGLNLAIPKESVDT 123 Query: 124 NLKTGALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIGKPVLAGIE 183 L ++L+ F+ H P S EAMA+NEILQIVVFS+FFG A +L + P++A + Sbjct: 124 GLAVSGMSLKGFLTHTIPTSITEAMASNEILQIVVFSMFFGIAGASLGEKFNAPLVAALN 183 Query: 184 GLSHVMLKITNYVMAFAPVGVFGAVAAVITAEGLGVLVVYAKLLGAVYLSLALLWVALIA 243 +SH+MLK+T YVM AP+ +F A+++VI ++GLG+L+ YA +G Y+++ L L+A Sbjct: 184 VVSHIMLKVTGYVMYVAPLAIFAAISSVIASQGLGILLNYASFIGGYYVAILLTSAVLLA 243 Query: 244 GGYFFLGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITGFVLPLGYS 303 GY L ++VFRLL M++ P+++ F T+SSE+AYPK +E+L FG I FVLP+GYS Sbjct: 244 VGYMVLKKEVFRLLNMLKDPVLVAFTTSSSEAAYPKTLERLVEFGCSRNIASFVLPIGYS 303 Query: 304 FNLDGSIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASLVVVAAVLP 363 FNL GS++Y SFAA+F+AQ Y + LS S+ M+L L++ SKGIAGVPR++LVV+AA +P Sbjct: 304 FNLVGSMVYCSFAAMFIAQAYNVQLSFSEITVMMLTLMLASKGIAGVPRSALVVLAATIP 363 Query: 364 MFGLPEAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSEGAIGAPVPEEADDP 419 F +P AGILL++GIDH LDMGR+ NVLGN IAT +++K+EG + V E P Sbjct: 364 SFNIPVAGILLLMGIDHFLDMGRSAINVLGNGIATAMLSKNEGQLQEEVLEAEAAP 419 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: 434 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: 436 Length of database: 424 Length adjustment: 32 Effective length of query: 404 Effective length of database: 392 Effective search space: 158368 Effective search space used: 158368 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