Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate 202182 SO3063 sodium:alanine symporter family protein (NCBI ptt file)
Query= SwissProt::P30145 (445 letters) >FitnessBrowser__MR1:202182 Length = 495 Score = 465 bits (1196), Expect = e-135 Identities = 237/431 (54%), Positives = 303/431 (70%), Gaps = 2/431 (0%) Query: 1 MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA 60 MIRL+ GKS++AGVSSFQAL M+L+GR+G GN+AG AT I +GGPGA+FWMW++ F+GA Sbjct: 43 MIRLMFDGKSTDAGVSSFQALAMTLAGRVGTGNIAGVATAITFGGPGALFWMWMVAFLGA 102 Query: 61 ATAYVESTWRKFIKRNKTDNTVAVRRSTLKKALAGNGLRCSRA-AIILSMAVLMPGIQAN 119 ++A+VEST + K ++K L + A A I + VL+PG+QAN Sbjct: 103 SSAFVESTLGQVYKEKINGEYRGGPAFYIEKGLGMKWYAWTFAIATIFACGVLLPGVQAN 162 Query: 120 SIADSFSNAFGIPKLVTGIFVIAVLGFTIFGGVKRIAKTAEIVVPFMAVGYLFVAIAIIA 179 SI S AF I VT + +LGF IFGGVKRIA A +VVPFMA+GY+ VA IIA Sbjct: 163 SIGASLKTAFDIDPNVTAAVLAMLLGFIIFGGVKRIANFATLVVPFMALGYIIVACVIIA 222 Query: 180 ANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVS 239 NI+++P + LI KSAFG D FG ILG A+MWGVKRG+Y+NEAGQGTG H ++AA V+ Sbjct: 223 LNIDQLPGILWLIIKSAFGFDAGFGAILGLAIMWGVKRGVYSNEAGQGTGPHASSAAAVT 282 Query: 240 HPAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEKTGETIVEHLKGVEPGAGYTQ 299 HPAKQGLVQAFS+Y+D V +AT M+L TG YNV G + + GV G+GY Q Sbjct: 283 HPAKQGLVQAFSVYIDTLFVCSATGFMLLITGLYNV-QGPDGAALYTGIAGVAAGSGYVQ 341 Query: 300 AAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFALKLVFLA 359 A++++ PGFG+ F+AIALFFFAFTT+ AYYYIAETN+AY+ R R LK++ +A Sbjct: 342 TAMESMMPGFGNMFVAIALFFFAFTTIVAYYYIAETNIAYINRKVNRPWLTVMLKVIIMA 401 Query: 360 ATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGKDPEFNA 419 +T YGTVKTA AW MGDIG+GIM WLN+IAI+LL K A+ LKDYE Q KQG +P+F+ Sbjct: 402 STVYGTVKTADLAWGMGDIGVGIMAWLNIIAIILLQKVAFTCLKDYESQQKQGIEPQFDP 461 Query: 420 SKYGIKNAKFW 430 K GI +A +W Sbjct: 462 EKLGIPHADYW 472 Lambda K H 0.324 0.137 0.407 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: 685 Number of extensions: 36 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: 445 Length of database: 495 Length adjustment: 33 Effective length of query: 412 Effective length of database: 462 Effective search space: 190344 Effective search space used: 190344 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 (21.5 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