Align Monocarboxylic acid transporter (characterized)
to candidate 18095 b4067 acetate permease (NCBI)
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__Keio:18095 Length = 549 Score = 439 bits (1128), Expect = e-127 Identities = 250/558 (44%), Positives = 350/558 (62%), Gaps = 40/558 (7%) Query: 8 AQDAVSEGVGNPILN---ISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGL 64 A DA+S V N I +F++F++ T+ + K +D+YT G + +G QNGL Sbjct: 18 AADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTAGGNITGFQNGL 77 Query: 65 AIAGDYLSAASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVL 124 AIAGDY+SAASFLGI + +GYDG +YS+GF V W + L L+AE LRN+GR+T ADV Sbjct: 78 AIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLRNLGRYTFADVA 137 Query: 125 SFRLRQKPVRVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMI 184 S+RL+Q P+R+ +ACG+L V YLIAQM GAG L+ +L ++ + V +VG++M+ Sbjct: 138 SYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN----YHIAVVLVGVLMM 193 Query: 185 AYVLLGGMKGTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAAT 244 YVL GGM TT+VQ+IKAVLL+ G + M + V L ++A+ H Sbjct: 194 MYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVH-------P 246 Query: 245 KGYDPTQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVT 304 KG D I++P G + + +SL L L GTAGLPH+LMRF+TV A+EARKSV Sbjct: 247 KGVD---IMKP----GGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299 Query: 305 WAIVLIGAFYLMTLVLGYGAAALVG--PDRVIAAP---GAANAAAPLLAFELGGSIFMAL 359 +A +G FY++T ++G+GA LVG P+ AA G N AA LA +GG++F+ Sbjct: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGF 359 Query: 360 ISAVAFATVLAVVAGLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIV 419 ISAVAFAT+LAVVAGL + ++AV HD+Y V + G +TE E++RVS+ITV+++G+I+I+ Sbjct: 360 ISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAII 418 Query: 420 LGILAMTQNVAFLVALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFL 479 LG+L QN+AF+V LAFA+AAS N P IL S+YW K T GA+ + GLI+A++L+ L Sbjct: 419 LGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMIL 478 Query: 480 SPAVSGNDSAMVPGADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEME--- 536 P + + G + AIFP + P L SI +AF+ W DN + A E E Sbjct: 479 GPTI----WVQILGHEKAIFPYEYPALFSITVAFLGIW---FFSATDNSAEGARERELFR 531 Query: 537 ---VRSLTGVGVEKAVDH 551 +RS TG GVE+ H Sbjct: 532 AQFIRSQTGFGVEQGRAH 549 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: 668 Number of extensions: 30 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: 551 Length of database: 549 Length adjustment: 36 Effective length of query: 515 Effective length of database: 513 Effective search space: 264195 Effective search space used: 264195 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