Align Monocarboxylic acid transporter (characterized)
to candidate BPHYT_RS11800 BPHYT_RS11800 acetate permease
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__BFirm:BPHYT_RS11800 Length = 528 Score = 410 bits (1053), Expect = e-119 Identities = 224/538 (41%), Positives = 334/538 (62%), Gaps = 26/538 (4%) Query: 21 LNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIV 80 L I FV FI +++ + + + ++ F+ G + S QNGLA+AGD++SA SFLG+ Sbjct: 10 LRIIAFVGFIGLSLVLTGWSARRSRGTSGFFVAGRNLSPFQNGLALAGDFMSAGSFLGVT 69 Query: 81 GAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACG 140 G +SL G+DG +Y +GF W++ +L+VAEP+RN G++T++DV++ RLR + VR A + Sbjct: 70 GLVSLFGFDGIVYQVGFIAGWIMIMLIVAEPVRNCGKYTLSDVVALRLRSRGVRAATSVS 129 Query: 141 TLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQM 200 +L +L YL+AQ+ G G+L S+LL I A +V ++GI+MIAYVL GGM TYVQ+ Sbjct: 130 SLITSLAYLLAQLVGGGALASLLLPIGT---NAAIV-LIGILMIAYVLFGGMVAATYVQI 185 Query: 201 IKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGLQYG 260 +KAVL+ A++ +L S + L N A P Q PG + Sbjct: 186 VKAVLVWTAGAVLVLLALAHFSFDVGALFNKA----------RLSSLHPAQYFVPGGYF- 234 Query: 261 ATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTLVL 320 LD +SL LAL LGTAGLPHV+ RFYTVP+A ARKS ++++ +F +M ++L Sbjct: 235 ---KDPLDTLSLTLALALGTAGLPHVMTRFYTVPSAVAARKSAKIGLIVMTSFAVMMILL 291 Query: 321 GYGAAALVGPDRVIAAPGAANAAAPLLAFELGGS-------IFMALISAVAFATVLAVVA 373 G+ A A+VGP ++A + N+A LLA LGG + +A +SA+AFAT+LAVV+ Sbjct: 292 GFSATAIVGPAAILATHSSGNSAITLLATTLGGGAGSAGGELLLACVSAIAFATILAVVS 351 Query: 374 GLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLV 433 G+ I++++ + HDI+ + + E QV +++I +V G+ ++ L +L T NVAFLV Sbjct: 352 GIMISSASTISHDIFGQLFSASRDKERRQVVIAKIATIVFGIAAMGLALLVKTFNVAFLV 411 Query: 434 ALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPG 493 LAFA+AASANLP IL+S+YW++F GAVAA+ G +S++ L+ L PAV G + Sbjct: 412 GLAFAIAASANLPVILFSMYWRRFTDRGAVAAVLAGTLSSIGLVLLGPAVIGAKGIIFKD 471 Query: 494 ADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGVGVEKAVDH 551 + F L NPGL SIP+ FIAGWIG++ + D ++R L+G+G E A +H Sbjct: 472 ST-PPFWLSNPGLFSIPVGFIAGWIGSVTTSQNAADTSFDAQQLRMLSGLGAEAASEH 528 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: 595 Number of extensions: 26 Number of successful extensions: 5 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: 528 Length adjustment: 35 Effective length of query: 516 Effective length of database: 493 Effective search space: 254388 Effective search space used: 254388 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: 52 (24.6 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