Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate 3606889 Dshi_0319 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__Dino:3606889 Length = 411 Score = 292 bits (748), Expect = 1e-83 Identities = 168/382 (43%), Positives = 229/382 (59%), Gaps = 8/382 (2%) Query: 2 RAWVFQVVTVVAVIALGWFLFDNTQTNLQHRGITSGFGFLERSAGFGIAQHLIDYTEADS 61 R + FQ + ++A+I +L N NL G F FL + A + I Q LI YT D+ Sbjct: 30 RGYTFQFIALIALIFFFGWLVSNAIYNLAALGQDINFSFLGQPASYEIDQTLIPYTSTDT 89 Query: 62 YARVFLIGLLNTLLVTFIGVILATILGFIIGVARLSQNWIISKLATVYVEVFRNIPPLLQ 121 + R +GLLNTLLV F+G I ATI G + GV RLS+NW+++K+ +VYVE+FRNIP L+ Sbjct: 90 HMRAAFVGLLNTLLVAFLGCITATIFGVLAGVLRLSKNWLVAKVMSVYVEIFRNIPVLIW 149 Query: 122 ILFWYFAVFLSMPGPRAAHN--------FGDTFFVSSRGLNMPAALVAEGFWPFVISVVL 173 I+ + ++P PRA D+ ++RG+ +PA + G V VL Sbjct: 150 IVIISAVMSQALPQPRAFRGEDATATMVLWDSVAFTNRGVYIPAPVWNPGSGIVVAVFVL 209 Query: 174 AIVAIVLMTRWANKRFEATGEPFHKFWVGLALFLVIPALSALLFGAPVHWEMPELKGFNF 233 +I+ I + R+A TG+ + LA+F V L+ + G P+ + PEL GFNF Sbjct: 210 SIIGIFVFRRYAKNLLFNTGKLLPVGRISLAIFFVPTLLAFFVMGRPIGLDYPELGGFNF 269 Query: 234 VGGWVLIPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVII 293 GG + L+AL AL +YT AFIAE VR+GI +VS GQTEAA +LG+R + +I+ Sbjct: 270 RGGINIRGTLIALWFALALYTGAFIAENVRAGILAVSKGQTEAAAALGMRPNRIMSLIIL 329 Query: 294 PQALRVIIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYL 353 PQALRVIIPP+ SQYLNL KNSSLAA IGY ++ G LNQTG++ E + + M YL Sbjct: 330 PQALRVIIPPVISQYLNLTKNSSLAAAIGYMDLTGTLGGVTLNQTGRSFECVLLLMLFYL 389 Query: 354 AISISISLLMNWYNKRIALIER 375 IS+SIS LMN YN + L ER Sbjct: 390 LISLSISALMNLYNNAVKLKER 411 Lambda K H 0.328 0.141 0.430 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: 410 Number of extensions: 22 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: 375 Length of database: 411 Length adjustment: 31 Effective length of query: 344 Effective length of database: 380 Effective search space: 130720 Effective search space used: 130720 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 (21.8 bits) S2: 50 (23.9 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