Align Monocarboxylic acid transporter (characterized)
to candidate WP_068865628.1 I603_RS12870 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_001677335.1:WP_068865628.1 Length = 591 Score = 153 bits (387), Expect = 2e-41 Identities = 100/308 (32%), Positives = 158/308 (51%), Gaps = 26/308 (8%) Query: 27 VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 ++++ V + L +G +++FY G + NG+A A D++SAASF+ + G Sbjct: 6 LIYLFVGASFALYIGIAIWSRAGSTSEFYVAGGGVNPVVNGMATAADWMSAASFISMAGI 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 I+ GYD +Y +G+ +++ LL+A LR G+FT+ D + R K RV A + Sbjct: 66 IAFTGYDASVYLMGWTGGYVLLALLLAPYLRKFGQFTVPDFIGTRYYSKAARVVAVICLI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 V+ Y+ QM G G + S LD+ VV+G +GIV + Y +LGGMKG TY Q+ + Sbjct: 126 LVSFTYIAGQMRGVGIVFSRFLDVD--ITTGVVIG-MGIVFV-YSVLGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSG------GLTTLLNDAVEKHAASDYAATKGYDPTQILEPG 256 +L+ + ++G GL + + D A+ Y K ++ G Sbjct: 182 FCVLIFAYMVPAFFLSFMITGNPVPQFGLGSKVGD-----ASGLYVLQK----LDLVLTG 232 Query: 257 LQYGATLTTQ---LDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAF 313 L + A Q +D + LAL +GTAGLPHV++RF+TVP A +AR S WA++ I Sbjct: 233 LGFAAYTAGQKSMIDVFCITLALMVGTAGLPHVIVRFFTVPKASDARLSAGWALIFIALL 292 Query: 314 YLMTLVLG 321 Y +G Sbjct: 293 YTTAPAVG 300 Score = 63.9 bits (154), Expect = 2e-14 Identities = 50/158 (31%), Positives = 75/158 (47%), Gaps = 10/158 (6%) Query: 357 MALISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLI 416 +AL++A A L+ AGL + SAAV HD+ R S + E + IG Sbjct: 403 IALVAAGGLAAALSTAAGLLLVISAAVSHDLLKQTFRPAISEKGELLAARLAATAAIG-- 460 Query: 417 SIVLGILAMTQN--VAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISAL 474 V G L + VA +VA AF +AA++ P IL ++ K+ N GA+A + +GL Sbjct: 461 --VAGYLGINPPGWVAQVVAFAFGLAAASLFPAILMGIFSKRMNREGAIAGMVSGLAFTF 518 Query: 475 LLIFLSPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLA 512 I VS + S A+W +F + G+ I +A Sbjct: 519 GYIVWFKLVSPDTST---AANW-LFGISPEGIGVIGMA 552 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: 674 Number of extensions: 42 Number of successful extensions: 5 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: 591 Length adjustment: 36 Effective length of query: 515 Effective length of database: 555 Effective search space: 285825 Effective search space used: 285825 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 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