Align Facilitated trehalose transporter Tret1; BmTRET1 (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= SwissProt::A9ZSY3 (505 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 168 bits (426), Expect = 3e-46 Identities = 129/435 (29%), Positives = 216/435 (49%), Gaps = 63/435 (14%) Query: 95 GLMPLAALVGGIVGGPL----IEYLGRKKTI-----------MGTAVPFTIGWMLIANAI 139 G+ +AL+G ++GG L LGR+ ++ +G+ P + + + Sbjct: 59 GITSSSALIGCVLGGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPNM 118 Query: 140 NVVMVF-AGRVICGVCVGIVSLAFPVYIGETIQPEVRGAL----------GLLPTAFGN- 187 ++++ F RV+ G+ VG+ S P+YI E +RG L G+L F N Sbjct: 119 DLLIAFNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNY 178 Query: 188 -------TGILLAFLVG-----------SYLDWSNLAFFGAAIPVPFF-LLMILTPETPR 228 I+L G + + F A P FF LL+ P+TPR Sbjct: 179 LIMGDHQNPIILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPR 238 Query: 229 WYVSKARVQEARKSLRWLRGKNVNIEKEMRDLTISQTESDRTGGNAFKQLFSKRYLPAVM 288 + V + ++A L + GK ++ + D I T ++T ++LF+ + ++ Sbjct: 239 YLVLVQQEEKAYTILEKINGKK-KAQEILND--IKATAQEKT-----EKLFTYG-VTVIV 289 Query: 289 ISLGLMLFQQLTGINAVIFYAASIFQMSGSSVDENLASIIIGVVNFISTFIATMLIDRLG 348 I + L +FQQ GINAV++YA IF+ +G+ + ++I+G+VN I T +A +DR G Sbjct: 290 IGILLSVFQQAIGINAVLYYAPRIFENAGAEGGGMMQTVIMGIVNIIFTLVAIFTVDRFG 349 Query: 349 RKVLLYISSVAMITTLLALGAYFYLKQNHIDVTAYGWLPLACLVIYVLGFSIGFGPIPWL 408 RK LL I S+ M A+GA+ + + + G LP+ +++Y F + +GPI W+ Sbjct: 350 RKPLLIIGSIGM-----AVGAFAVAMCDSMAIK--GVLPVLSIIVYAAFFMMSWGPICWV 402 Query: 409 MLGEILPSKIRGTAASLATGFNWTCTFIVTKTFQNIIDAIYMHGTLWLFAVICIGGLLFV 468 ++ EI P+ IRG A ++A F W +IV+ TF + D M L+ +IC+ +FV Sbjct: 403 LISEIFPNTIRGKAVAIAVAFQWIFNYIVSSTFPALYDFSPMF-AYSLYGIICVAAAIFV 461 Query: 469 IFFVPETKGKSLEEI 483 +VPETKGK+LE++ Sbjct: 462 WRWVPETKGKTLEDM 476 Score = 33.5 bits (75), Expect = 2e-05 Identities = 45/160 (28%), Positives = 71/160 (44%), Gaps = 23/160 (14%) Query: 280 SKRYLPAV--MISLGLMLFQQLTGINA-------VIFYAASIFQMSGSSVDENLASIIIG 330 SK YL ++ + LG +LF T + + F +AS FQ + +S +IG Sbjct: 9 SKLYLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKVMHGITSSSALIG 68 Query: 331 VVNFISTFIATMLIDRLGRKVLLYISSVAMITTLLALGAYFYLKQNHIDVTAYGWLPLAC 390 V + ++ + RLGR+ L +++V L ALG+Y+ + YG + Sbjct: 69 CV--LGGALSGVFASRLGRRNSLRLAAVLFF--LSALGSYY----PEVLFFEYGKPNMDL 120 Query: 391 LVIYVL-----GFSIGFGPIPWLM-LGEILPSKIRGTAAS 424 L+ + L G +G M + EI PS IRGT S Sbjct: 121 LIAFNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVS 160 Lambda K H 0.325 0.140 0.420 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: 597 Number of extensions: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 505 Length of database: 484 Length adjustment: 34 Effective length of query: 471 Effective length of database: 450 Effective search space: 211950 Effective search space used: 211950 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 (21.6 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