Align Uncharacterized protein (characterized, see rationale)
to candidate WP_045582999.1 AL072_RS17490 dicarboxylate/amino acid:cation symporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >NCBI__GCF_001305595.1:WP_045582999.1 Length = 425 Score = 508 bits (1307), Expect = e-148 Identities = 252/413 (61%), Positives = 329/413 (79%), Gaps = 1/413 (0%) Query: 3 LNRLPTLIFIAMLLGVLAGTAAHHYAPDPAAAKSIADHLSILTDVFLRMIKMIIGPLVFA 62 +N+ TLI +AMLLG++ G A + DPAAAK IA + +++TD+FLR+IKMII PL+F+ Sbjct: 1 MNKQTTLIIVAMLLGIVTGYACNSLF-DPAAAKDIAGYFAMVTDIFLRLIKMIIAPLIFS 59 Query: 63 TLVSGIASMGDGKAVGRIGMKAMAWFIAASITSLLLGLLMANLLRPGDGMNLALPAADAA 122 TLV+G+A MGD + VGRIG KA+ WF+ AS SL +GL+ ANLL+PG + + LP A A+ Sbjct: 60 TLVAGMAGMGDARTVGRIGGKAVGWFLMASFASLFIGLIFANLLQPGANVGVPLPDAGAS 119 Query: 123 SNLKTGALNLREFIAHMFPKSFVEAMATNEILQIVVFSLFFGFALGTLKDGIGKPVLAGI 182 + LKT ALNL++F+ H+FP++F EAMA NEILQI++FS+F G A+G L+D + I Sbjct: 120 AGLKTSALNLKDFLTHVFPRNFFEAMANNEILQILIFSIFVGLAIGQLRDTKAGLLARSI 179 Query: 183 EGLSHVMLKITNYVMAFAPVGVFGAVAAVITAEGLGVLVVYAKLLGAVYLSLALLWVALI 242 E + VMLK+T+YVM FAP+GVF AVA V+T +GLGVL+VY K +G+ Y++LA+LW L+ Sbjct: 180 EEVVPVMLKVTDYVMRFAPIGVFAAVANVVTTQGLGVLLVYGKFMGSFYVALAVLWAVLV 239 Query: 243 AGGYFFLGRDVFRLLKMVRAPLMIGFATASSESAYPKVIEQLGRFGVKERITGFVLPLGY 302 G+ L DVFR++K +R P+++GF+TASSESAYP+V+E+L GV+ER+ GFVLPLGY Sbjct: 240 FAGFVVLKGDVFRVVKAMRQPMLLGFSTASSESAYPRVMEELKTLGVRERVIGFVLPLGY 299 Query: 303 SFNLDGSIMYTSFAALFVAQVYGIHLSLSQQVTMLLVLLVTSKGIAGVPRASLVVVAAVL 362 SFNLDGS++YT+FA+LF+AQ YGI L+L QQ+ MLLVL+V+SKGIAGVPR+SLVVVAAVL Sbjct: 300 SFNLDGSMIYTAFASLFIAQAYGIPLTLEQQIVMLLVLMVSSKGIAGVPRSSLVVVAAVL 359 Query: 363 PMFGLPEAGILLVLGIDHVLDMGRTVTNVLGNAIATTVVAKSEGAIGAPVPEE 415 PMF LPEAG+LL++GIDH LDMGRT TNVLGN IATTVVAK E AIG EE Sbjct: 360 PMFHLPEAGVLLIMGIDHFLDMGRTATNVLGNGIATTVVAKWENAIGTEEDEE 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: 519 Number of extensions: 20 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: 425 Length adjustment: 32 Effective length of query: 404 Effective length of database: 393 Effective search space: 158772 Effective search space used: 158772 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 24 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