Align Monocarboxylic acid transporter (characterized)
to candidate GFF346 Psest_0347 probable sodium:solute symporter, VC_2705 subfamily
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__psRCH2:GFF346 Length = 589 Score = 146 bits (369), Expect = 2e-39 Identities = 87/293 (29%), Positives = 145/293 (49%), Gaps = 5/293 (1%) Query: 23 ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 I++ V + + + V + +FY G NG+A A D++SAASF+ + G Sbjct: 6 INMLFVGASFLLYIGIAVWARAGSTKEFYVAGGGVHPVTNGMATAADWMSAASFISMAGL 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 I+ GY +Y +G+ +++ +L+A LR G+FT+ D + R + R+ A + Sbjct: 66 IASGGYATSVYLMGWTGGYVLLAMLLAPYLRKFGKFTVPDFIGDRFYSRGARLTAVVCLI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 +++ Y+I QMAGAG S L++ + + I ++ AY + GGMKG TY Q+ + Sbjct: 126 LISVTYVIGQMAGAGVAFSRFLEVS----NSAGIWIAAAIVFAYAVFGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYGAT 262 ++L+ I V ++++G + H S D Y A Sbjct: 182 YIVLIIAYTIPAVFIAMQLTGNPIPMFG-MFGTHVDSGVPLLDKLDQVVTDLGFAAYTAD 240 Query: 263 LTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYL 315 + +L+ L+L +GTAGLPHV++RF+TVP +AR S W +V I YL Sbjct: 241 VDNKLNMFLFTLSLMIGTAGLPHVIIRFFTVPKVADARWSAGWTLVFIALLYL 293 Score = 72.0 bits (175), Expect = 6e-17 Identities = 61/201 (30%), Positives = 100/201 (49%), Gaps = 12/201 (5%) Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416 + LI+A A A L+ AGL + S+A+ HD+ +I N + +E ++ +R+++ L+ Sbjct: 395 IGLIAAGAIAAALSTAAGLLLAISSAISHDLIKTLI-NPKISEKNEMLAARLSMTAAILL 453 Query: 417 SIVLGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLL 476 + LG L A +VALAF +AA++ P ++ ++ K+ N+ GAVA + G+IS + Sbjct: 454 ATWLG-LNPPGFAAQVVALAFGLAAASLFPALMMGIFSKRVNSKGAVAGMLVGVISTAVY 512 Query: 477 IFLSPA---VSGNDS-AMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLV--GKPDNMDD 530 IFL + G S P W + G V L F + ++ P + D Sbjct: 513 IFLYLGWFFIPGTASIPNTPDQWWMGISPQAFGAVGAMLNFAVAYAVSMATEAPPQEIQD 572 Query: 531 LAAEMEVRSLTGVGVEKAVDH 551 L VR+ G GV A+DH Sbjct: 573 LVE--SVRTPKGAGV--ALDH 589 Lambda K H 0.324 0.138 0.393 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: 640 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 589 Length adjustment: 36 Effective length of query: 515 Effective length of database: 553 Effective search space: 284795 Effective search space used: 284795 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: 53 (25.0 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