Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate 3606890 Dshi_0320 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >FitnessBrowser__Dino:3606890 Length = 432 Score = 284 bits (727), Expect = 3e-81 Identities = 165/417 (39%), Positives = 237/417 (56%), Gaps = 61/417 (14%) Query: 8 PDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTTRA 67 P PPP S +G+V W+R+N+F S +++LTL IY + L+ W + + W + Sbjct: 17 PPSPPPVSEVGIVNWLRSNLFYSIPSSILTLLTAAFIYWLSSILMPW-MFNGVWDANSIR 75 Query: 68 DCTKE-----GACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPRKA 122 DC + G C+ I +R+ Q ++G YP + WR L + +AP+ + PRK Sbjct: 76 DCREILDGAIGGCFAVIAERWPQLIFGNYPNEEYWRAVLAFVGLFVALAPVLFFKLPRKM 135 Query: 123 IYG------LSFLVLYPISAWC---LLHGGVFG--------------------------- 146 ++ +++ +++ SAW L G V G Sbjct: 136 LWFTGLFPFIAYWLIWGGSAWVSVMALVGVVVGYVAFKALEERSFFGAIVAALFATLLFW 195 Query: 147 ------------------LDAVATSQWGGLMLTLVIATVGIVGALPLGIVLALGRRSNMP 188 L V + GG M+ ++ T GI +LPLGI LALGR+SN+P Sbjct: 196 IFISPLAVNALSSVVALSLPQVESRFIGGFMINFILGTSGIALSLPLGIALALGRQSNLP 255 Query: 189 AIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILFQSAYIAEV 248 I+ VCV FIEF RGVPLIT+LF++SVML FLP G +FD +LR +I + LF SAYIAE Sbjct: 256 IIKGVCVVFIEFIRGVPLITLLFVASVMLAYFLPPGTSFDLVLRVIIMITLFASAYIAEA 315 Query: 249 VRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIII 308 +RGGL A+P+GQYEA ++GL YW+SM L+ILPQALK+ IP IVN I LFKDT+LV II Sbjct: 316 IRGGLAALPRGQYEAGDSLGLDYWQSMRLIILPQALKISIPSIVNIAIGLFKDTTLVSII 375 Query: 309 GLFDLLNSVK-QAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLDTGHK 364 +FD+L ++ + +W G+ E FA ++F++FC+G+S+YS LER+L T H+ Sbjct: 376 SMFDMLGMIQGPILSSTEWFGVYWELLGFAGVLFFVFCYGISQYSQWLERQLATEHR 432 Lambda K H 0.330 0.144 0.469 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: 655 Number of extensions: 47 Number of successful extensions: 6 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: 365 Length of database: 432 Length adjustment: 31 Effective length of query: 334 Effective length of database: 401 Effective search space: 133934 Effective search space used: 133934 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 (21.9 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