Align 2-deoxy-D-ribonate transporter 1 (characterized)
to candidate HSERO_RS05805 HSERO_RS05805 MFS transporter
Query= reanno::WCS417:GFF1429 (438 letters) >FitnessBrowser__HerbieS:HSERO_RS05805 Length = 447 Score = 334 bits (857), Expect = 3e-96 Identities = 175/428 (40%), Positives = 251/428 (58%), Gaps = 5/428 (1%) Query: 12 ALNKLMFVKLMPLLIIAYILSFLDRTNIALAKHHLDVDLGISAAAYGLGAGLFFLTYALS 71 A++K+ + +++PL + +I++++DR NI + HL DLGI AAA+GLGAGLFF+ YAL Sbjct: 17 AVSKIKW-RILPLFVAMFIINYIDRVNIGFVRSHLSTDLGIGAAAFGLGAGLFFVGYALF 75 Query: 72 EIPSNLIMHKVGARFWIARIMVTWGLISAAMAFVQGETSFYVLRLLLGIAEAGLFPGVML 131 E+PSN+++ + GAR W+ RIM TWGL++A MAFVQ ETSFY +R LLG+AEAG FPGV+ Sbjct: 76 EVPSNMLLQRYGARAWLTRIMFTWGLVAACMAFVQSETSFYFMRFLLGVAEAGFFPGVVY 135 Query: 132 YLTYWFNREQRARATGYFLLGVCFANIIGGPVGAALMRMDGMLGWHGWQWMFMLEGLPAV 191 Y T W +R RA FL G A+I+ GP+ AL+ ++G G HGWQWMF++EG ++ Sbjct: 136 YFTQWLPNHERGRAMAVFLSGSAIASILSGPITGALLLIEGG-GLHGWQWMFIIEGGASM 194 Query: 192 AFAWVVWRKLPDRPSKAPWLSAEEARGIEQRIAQETEE-GAGEGGH--SLKNWLTPQILL 248 F VVW L P +A WLS E+ + IA E E+ A H +L PQI+L Sbjct: 195 VFCVVVWLVLDSTPREAKWLSQEQREALAAVIAAEQEQRAANRPAHVSALSLLRDPQIVL 254 Query: 249 AIFVYFCHQITIYTVIFFLPSIISKYGELSTMSVGLLTSLPWIAAALGALLIPRFATTPG 308 F+YF Q+TIY F+LP+II K G + VGL S+PWI A L A Sbjct: 255 FCFIYFAIQLTIYGATFWLPTIIKKMGHFNDFQVGLFNSIPWIVAIAAMYLFAVLAARYK 314 Query: 309 RCRRLLVTGLLTMALGLGIASVSGPVFSLLGFCLSAVMFFVVQSIIFLYPASRLKGVALA 368 + + + T L+ A G+ I++V+GPV + C + + F S+ + P + L A Sbjct: 315 KPQFWVATTLVISAAGMAISAVAGPVIGFVAVCFAGIGFKAASSLFWPIPQAYLDARIAA 374 Query: 369 GGLGFVNACGLLGGFVGPSVMGVIEQSTGNAMNGLKVIALVLVVAALAALRLRMGHEPER 428 L +N+ G LGGF P+ G +EQ TG+ GL ++ ++AA+ R Sbjct: 375 AVLALINSLGNLGGFFAPATFGYLEQKTGSIQGGLFALSGASLLAAVLVFLARTRPAAPD 434 Query: 429 GAQASEAS 436 G +EA+ Sbjct: 435 GGGPAEAA 442 Lambda K H 0.327 0.141 0.438 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: 567 Number of extensions: 28 Number of successful extensions: 3 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: 438 Length of database: 447 Length adjustment: 32 Effective length of query: 406 Effective length of database: 415 Effective search space: 168490 Effective search space used: 168490 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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