Align Sodium-coupled monocarboxylate transporter 1; Electrogenic sodium monocarboxylate cotransporter; zSMCTe; Sodium solute symporter family 5 member 8 protein; Solute carrier family 5 member 8 (characterized)
to candidate Ga0059261_0571 Ga0059261_0571 transporter, SSS family
Query= SwissProt::Q3ZMH1 (610 letters) >FitnessBrowser__Korea:Ga0059261_0571 Length = 793 Score = 186 bits (471), Expect = 4e-51 Identities = 140/467 (29%), Positives = 240/467 (51%), Gaps = 26/467 (5%) Query: 10 TFSVWDYVVFAGLILVAAGIGLFQSFRGRKEASSDEFLLGGRQMTAVPVALSLTASFMSG 69 + ++ D+++ + G+G F +RG K SS+EF LG R + A +S+ A +S Sbjct: 299 SLALLDWLIIGVYMFGMLGVG-FYFYRGAKNGSSNEFFLGSRSIPAWAAGISMFAGSISS 357 Query: 70 ITVIGTPAEAYLYGTPFWLFFISYAIMSTISAEIFV-----PLFYRLNITSTYEYLEMRY 124 I+ + PA+AY W + +S MSTI+ IFV PLF RLN+ S + YLE R+ Sbjct: 358 ISYLAIPAKAYETN---WQYIMSK--MSTIAGLIFVAIMIVPLFRRLNLVSVFNYLETRF 412 Query: 125 NKLIRVIGTSMYII-QTALYTGMVIFAPALALNQITGLDLWGVLVATGAVCIIYCTLGGL 183 + IR++ ++++++ Q G+V+F PA+A+ IT ++ +V G IIY LGG+ Sbjct: 413 HPSIRLLSSALWMLMQIGGRMGIVLFLPAMAIGTITDTNIVACIVVVGIFTIIYTALGGM 472 Query: 184 KAVIWTDVFQMIIMLGGFVAVIARGAVL-QGGLGRVWND--SFYGGRLETFSFDPDPLRR 240 KAV+WTDVFQ++++ GG A A G ++ Q GL V +F + SFD + + Sbjct: 473 KAVVWTDVFQVMVLTGG--ACFAIGFIIYQLGLMPVVETARAFEKTDMVNLSFD---ITQ 527 Query: 241 HSFWTIVVGGSLMWASMYSINQSQVQRYISCRTMTHAKLSLYVNMVGLWVTVSLAMMSGL 300 + W ++ + +Q +QR ++ + A S++V V L + + + G Sbjct: 528 PTLWGFLILVLFDVVLTFPKDQVLMQRVLATPSEKEASRSVWVFAVVLLPSAFMFYIIGT 587 Query: 301 TMYSIYKDCDPFTNKDVGATDQLLPYLVMDILADFPGLPGLFVAAAYSGTLSTVSSSINA 360 +++ Y++ +P + D + P + L G+ GL +A ++ + T+S IN+ Sbjct: 588 VLFAYYRE-NPAQLNPMLPIDAVFPAFIGTELP--AGVTGLIIAGLFAAAMGTLSGIINS 644 Query: 361 LVAVTVEDFMKPAWPSLTERQLSWINMGMSVFYGAVCIGMAGVASMMG--NILQAALSIF 418 + + DF + + T+ Q MSV G + IG+A + S M ++L + +F Sbjct: 645 VATLLSVDFY-GKFRNPTQEQTVRFAEWMSVVVGLIGIGIAIILSRMDIHSLLDLTIELF 703 Query: 419 GMISGPLLGLYMLGMFFRCANSTGGLAGLASGLAITLWVGIGAQLYP 465 G++ G G Y LGMF R AN G G+ + +TL V I ++P Sbjct: 704 GLLGGSCAGAYTLGMFTRRANWQGVAIGIVAASLLTLVVWIFGLIHP 750 Lambda K H 0.324 0.138 0.420 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: 1153 Number of extensions: 68 Number of successful extensions: 6 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: 610 Length of database: 793 Length adjustment: 39 Effective length of query: 571 Effective length of database: 754 Effective search space: 430534 Effective search space used: 430534 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: 54 (25.4 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