Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_011840330.1 RSPH17029_RS02010 amino acid ABC transporter permease
Query= reanno::pseudo6_N2E2:Pf6N2E2_5404 (365 letters) >NCBI__GCF_000015985.1:WP_011840330.1 Length = 442 Score = 317 bits (813), Expect = 3e-91 Identities = 178/429 (41%), Positives = 243/429 (56%), Gaps = 70/429 (16%) Query: 5 TFKPDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGT 64 T P + PP + GVV+WMR N+FS +N LTL IY ++ +V W ++ + W Sbjct: 15 TMLPPVAPPANEAGVVSWMRQNLFSGPLNIALTLLGLVAIYYVLEGIVPW-LMRSVWTAD 73 Query: 65 TRADCTK----------EGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLF 114 T A C + GACW I++R+ QF+YG+YP L WR LT L + +AP+ Sbjct: 74 TLAQCRQIITERWGEGATGACWAVIRERWPQFLYGFYPNHLYWRPTLTFLLLFVALAPIL 133 Query: 115 ISRFPRKAIY---------------GLSFL------------------------------ 129 ++ PR+ ++ G FL Sbjct: 134 FAQVPRQMLWFSLAYPFLAFWLLWGGSIFLPLVAAAGFLFGWLAYRLAARFGTIAAVAAA 193 Query: 130 VLYPISAWCLLHGGV-------------FGLDAVATSQWGGLMLTLVIATVGIVGALPLG 176 L P+ W L G V L+ V + ++GG +L + I GI +LPLG Sbjct: 194 ALVPVLWWLFLAGDVSDDLARLTGRTFPLWLEEVRSDKFGGFVLAVTIGVSGIALSLPLG 253 Query: 177 IVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIG 236 I+LALGRRS+M I+ + V+FIEF RGVPLI +LF +S++L FLP G FD +LR +I Sbjct: 254 IILALGRRSDMFLIKALSVSFIEFIRGVPLIALLFTASLLLNYFLPPGTTFDIILRVIIM 313 Query: 237 VILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFI 296 V LF +AYIAEV+RGGL A+P+GQYEAA A+GL YW++ L+ILPQALK+ IPGIV+TFI Sbjct: 314 VTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWKAQRLIILPQALKISIPGIVSTFI 373 Query: 297 ALFKDTSLVIIIGLFDLLNSVKQAA-ADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHL 355 +FKDT+LV+ +GL D L + A A W G+ E Y+F L+F+ F F MSRYSMHL Sbjct: 374 GMFKDTTLVVFVGLLDPLKGITDAVRASTDWKGIYWEPYIFVGLIFFAFNFAMSRYSMHL 433 Query: 356 ERKLDTGHK 364 ER+L T H+ Sbjct: 434 ERRLKTDHR 442 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: 39 Number of successful extensions: 4 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: 442 Length adjustment: 31 Effective length of query: 334 Effective length of database: 411 Effective search space: 137274 Effective search space used: 137274 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 Apr 10 2024. 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