Align D-lactate transporter, permease component 1 (characterized)
to candidate GFF3452 PS417_17670 ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >FitnessBrowser__WCS417:GFF3452 Length = 336 Score = 155 bits (393), Expect = 1e-42 Identities = 117/390 (30%), Positives = 185/390 (47%), Gaps = 72/390 (18%) Query: 7 KDKTLLLVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLT 66 + K +LL V + + P IL P+ + L +IF + A+ N+L G T Sbjct: 13 QSKAMLLWVLAVLIGLPLIL---PSAT-----------LATEILIFAMAALACNLLLGYT 58 Query: 67 GYLSFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFS 126 G LSFG F G G+Y A + L + + A++ + I G AL++G +++RR+GIYF Sbjct: 59 GLLSFGQGIFFGAGAYCAALLMIHLQLGLFTALLGAAIAGGFLALLVGALAIRRTGIYFV 118 Query: 127 ILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEMRS 186 +LTLAF+QM++ +AY+ L+ T G+ GL L++ P + + T L L Sbjct: 119 MLTLAFSQMAYFVAYT-LSDWTGGDNGL-LSVPRPEI---------RLGETVLLSLADAR 167 Query: 187 TFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNT 246 F Y A++ L F + R+ SPFG L A++ N+ R + G +T Sbjct: 168 AF--------------YAFVAVLFLLIFIGARRVIASPFGSTLMAIRENETRASAIGYDT 213 Query: 247 RPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLG 306 R + + FV+SG G+AG L A + + S +++MTI+GG G+L G +LG Sbjct: 214 RHFKILVFVLSGAVTGIAGALYAMLLHFVPLSNIDLMMSENILIMTIVGGTGSLFGSLLG 273 Query: 307 AGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLVVIF 366 AG I + S + W W + LG++ +LVVIF Sbjct: 274 AGSIVLLGDFLSDL-------W---------------------PRWLMLLGVILILVVIF 305 Query: 367 LPGGLVEGGQKLRGWIQGRK-----AKKDG 391 + GGL G L ++G + AK++G Sbjct: 306 MRGGLWGGLVSLFERVRGSRKTAAVAKEEG 335 Lambda K H 0.327 0.143 0.435 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: 389 Number of extensions: 25 Number of successful extensions: 3 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: 400 Length of database: 336 Length adjustment: 30 Effective length of query: 370 Effective length of database: 306 Effective search space: 113220 Effective search space used: 113220 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: 49 (23.5 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