Align Monocarboxylic acid transporter (characterized)
to candidate WP_082908435.1 BJL86_RS04300 cation acetate symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_001659785.1:WP_082908435.1 Length = 540 Score = 720 bits (1858), Expect = 0.0 Identities = 369/538 (68%), Positives = 440/538 (81%), Gaps = 12/538 (2%) Query: 14 EGVGNPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSA 73 E VG+ +LN+ VF +FI++TM +V+R ST + DFYT FSGTQNG AIAGDYLSA Sbjct: 15 EAVGSTVLNMVVFGIFIVITMGLVIRASNSTKSAADFYTASGGFSGTQNGFAIAGDYLSA 74 Query: 74 ASFLGIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPV 133 ASFLGI GAI+L GYDGFLYSIGF VAWLVALLLVAE +RN GRFTMADVLSFRL+Q+PV Sbjct: 75 ASFLGIAGAIALQGYDGFLYSIGFLVAWLVALLLVAELMRNTGRFTMADVLSFRLQQRPV 134 Query: 134 RVAAACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMK 193 R+AAA TLAV LFYLIAQMAGAG LV++LL+I Q+VVV IVG++MI YVL+GGMK Sbjct: 135 RMAAALATLAVCLFYLIAQMAGAGGLVALLLNIDSETGQSVVVAIVGVLMILYVLIGGMK 194 Query: 194 GTTYVQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQIL 253 GTTYVQMIKAVLLVGGV +M +L V V G + LL+ A+ + + Sbjct: 195 GTTYVQMIKAVLLVGGVLVMCLLVLVAVRGNFSELLSAAINRSGEP------------LT 242 Query: 254 EPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAF 313 +PGL+YGAT TT+LDF+SL +AL GTAGLPHVLMRFYTVPTAKEAR+SVTWAI LIGAF Sbjct: 243 DPGLKYGATETTKLDFLSLGIALVFGTAGLPHVLMRFYTVPTAKEARRSVTWAIALIGAF 302 Query: 314 YLMTLVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVA 373 YL TLVLG+GAAA+VG D + AAPG N+AAPLLA+ LGG IFM +ISAVAFAT+LAVVA Sbjct: 303 YLFTLVLGFGAAAMVGSDVIEAAPGGVNSAAPLLAYALGGEIFMGIISAVAFATILAVVA 362 Query: 374 GLAITASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLV 433 GLAI+ASA++ HDIYN VI++G++TE +Q++VSRITVVVIG++SIVLGI AM QN+AFLV Sbjct: 363 GLAISASASLAHDIYNGVIKHGKATEQQQLKVSRITVVVIGIVSIVLGIGAMGQNIAFLV 422 Query: 434 ALAFAVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPG 493 ALAFAVAASANLPTI+YSL+W++FNT GA+ +IY GLIS L+LIF SPA+SG+++AM+P Sbjct: 423 ALAFAVAASANLPTIIYSLFWRRFNTRGALFSIYGGLISTLVLIFFSPAISGSETAMLPN 482 Query: 494 ADWAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGVGVEKAVDH 551 ADWAIFPL NPG++SIP F+ G IGT +GK D D AEMEVRS+TGVGVEKAV H Sbjct: 483 ADWAIFPLSNPGIISIPFGFLMGIIGTFLGKSDEFPDKEAEMEVRSMTGVGVEKAVQH 540 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: 758 Number of extensions: 27 Number of successful extensions: 2 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: 540 Length adjustment: 35 Effective length of query: 516 Effective length of database: 505 Effective search space: 260580 Effective search space used: 260580 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 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