Align Uncharacterized protein (characterized, see rationale)
to candidate CA265_RS10595 CA265_RS10595 dicarboxylate/amino acid:cation symporter
Query= uniprot:A0A0C4Y5S4 (436 letters) >FitnessBrowser__Pedo557:CA265_RS10595 Length = 458 Score = 419 bits (1076), Expect = e-121 Identities = 203/370 (54%), Positives = 282/370 (76%), Gaps = 1/370 (0%) Query: 39 DHLSILTDVFLRMIKMIIGPLVFATLVSGIASMGDGKAVGRIGMKAMAWFIAASITSLLL 98 ++ ++L+D+FLR+IKMI+ PLVF TLV G+A +GD KAVGRIG K + WF+A S+ SL+L Sbjct: 87 EYFTLLSDIFLRLIKMIVAPLVFTTLVVGVAKVGDIKAVGRIGGKTLGWFLAMSLMSLVL 146 Query: 99 GLLMANLLRPGDGMNLALPAADAASNLKTGALNLREFIAHMFPKSFVEAMATNEILQIVV 158 G+++ NL PG M L+LP + ++ A+++++FIAH+FPKS E+M+TNEILQIVV Sbjct: 147 GMVLVNLFEPGRHMKLSLPDQLVNTGIQKAAMSVKDFIAHVFPKSIAESMSTNEILQIVV 206 Query: 159 FSLFFGFALGTLKDGIGKPVLAGIEGLSHVMLKITNYVMAFAPVGVFGAVAAVITAEGLG 218 FSLFFG A + D +G+ V+ + ++HV+LK+T YVM FAP+ VFGA+ A++ +GL Sbjct: 207 FSLFFGVATAAIGD-LGQIVIKAFDAIAHVILKMTGYVMNFAPLAVFGAMTAIVAKQGLN 265 Query: 219 VLVVYAKLLGAVYLSLALLWVALIAGGYFFLGRDVFRLLKMVRAPLMIGFATASSESAYP 278 VL YA +G YL LA+LW LI G+ L + +FRL+ ++ P ++ F+TASSE+AYP Sbjct: 266 VLNTYAIFIGEFYLGLAILWAVLIFLGFLVLKKRIFRLVNDMKEPALLAFSTASSEAAYP 325 Query: 279 KVIEQLGRFGVKERITGFVLPLGYSFNLDGSIMYTSFAALFVAQVYGIHLSLSQQVTMLL 338 K + L RFG K++I FVLPLGYSFNLDGS+MY +FA+LF+AQ YGIHL QQ++MLL Sbjct: 326 KTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYMTFASLFIAQAYGIHLGFEQQISMLL 385 Query: 339 VLLVTSKGIAGVPRASLVVVAAVLPMFGLPEAGILLVLGIDHVLDMGRTVTNVLGNAIAT 398 +L++TSKGIAGVPRASLVV+A + F +PEAG+ L++GID +LDMGR+ TNV+GN+IAT Sbjct: 386 ILMLTSKGIAGVPRASLVVIAGTIASFNIPEAGLALLIGIDPLLDMGRSATNVVGNSIAT 445 Query: 399 TVVAKSEGAI 408 VV+K EG + Sbjct: 446 AVVSKWEGEL 455 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: 492 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 436 Length of database: 458 Length adjustment: 33 Effective length of query: 403 Effective length of database: 425 Effective search space: 171275 Effective search space used: 171275 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