Align Ectoine/proline transporter ProP (characterized)
to candidate H281DRAFT_02725 H281DRAFT_02725 MFS transporter, MHS family, proline/betaine transporter
Query= SwissProt::Q79VC4 (504 letters) >FitnessBrowser__Burk376:H281DRAFT_02725 Length = 429 Score = 219 bits (558), Expect = 2e-61 Identities = 136/420 (32%), Positives = 221/420 (52%), Gaps = 25/420 (5%) Query: 33 IKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGGLVL 92 I T +GN +E+YD +YGY T++ +F + LL + FA+SYL RP+G LVL Sbjct: 24 IVATSIGNALEFYDLVVYGYFASTLSRLFFPTHDRTVSLLLTLGTFALSYLARPVGALVL 83 Query: 93 GPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEYA 152 G D+ GR+ L +++ +M + T L+ ++P A+IG A +L++L +++QGFS GGE+ Sbjct: 84 GSYSDRHGRKASLTLSIGLMTLGTGLVAVMPPYATIGIAAPILIFLSRLLQGFSAGGEFG 143 Query: 153 GATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTW--VTTHFYGATAMEDFGW 210 +T ++ E AP R GF M S+ + GAS + + + + T +E +GW Sbjct: 144 SSTAFLVEHAP-ARSGF------MSSWQFSSQGASTLLASLFGALLTGLLTPPQLEGWGW 196 Query: 211 RIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWR 270 RIPFL + +G I +Y+R R+ ETP F + + V V+ Sbjct: 197 RIPFLFGMLIGPIGLYIRRRMDETPEFARAEKLASPV--------------RVVLATQKE 242 Query: 271 PLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWS 330 +L+ I + T TA Y L YMP Y Q+ L +S T+ +M L+P VG S Sbjct: 243 RVLVSIGSLVLTTTANYMLL-YMPTYATHQLKLSPSSGFIATLVAGFIMMALVPVVGHLS 301 Query: 331 DRVGRKPVYATAVAATLILMVPAFLIMNT-GTIGAVLIALSMVAIPTGLYVALSASALPA 389 D++GR + L+ + PAF++MN ++ +L + VA+ Y A + + Sbjct: 302 DKLGRIRIMLPVGVLFLVTVYPAFMLMNAYPSLPMLLACVIWVALLKATYFAPIPALMAD 361 Query: 390 LFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALLF 449 LFP +R +GM +YNI ++FGG TP++ L+ T ++ P LY+M + I+ L++ Sbjct: 362 LFPVETRTTGMAFAYNIGTTIFGGFTPVVVAALIAFTHNNLAPGLYLMIAAVISLFTLMW 421 Lambda K H 0.322 0.138 0.407 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: 581 Number of extensions: 45 Number of successful extensions: 4 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: 504 Length of database: 429 Length adjustment: 33 Effective length of query: 471 Effective length of database: 396 Effective search space: 186516 Effective search space used: 186516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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