Align Aspartate/Glutamate transporter of 488 aas and 12 TMSs, AcaP (characterized)
to candidate WP_022528465.1 L248_RS02440 APC family permease
Query= TCDB::F2HJG8 (488 letters) >NCBI__GCF_000469325.1:WP_022528465.1 Length = 554 Score = 328 bits (842), Expect = 2e-94 Identities = 168/483 (34%), Positives = 283/483 (58%), Gaps = 19/483 (3%) Query: 6 IRWFTVAFIAFNMVWGMGNVVNNFAQQGITVVTSWLLILALYFIPYALIVGQLGSTFKDS 65 I W VA + F V G +++ NF QG+ VTSW+L+ LY IPY+LIV LGSTF Sbjct: 12 IPWVVVALMDFVTVIGFDDIIYNFRNQGLVAVTSWVLMTFLYVIPYSLIVAHLGSTFSAD 71 Query: 66 KGGVSSWVENTSTKRLAYYAAWTYWVVHIPYLAQKPQAILIAFGWVGQGNGNLVSQMSMT 125 GG++SWV T+ L Y+AAW YW+ +PY+ +++I+FGW+ G+G++ S M+ Sbjct: 72 AGGITSWVRETNGDTLGYFAAWFYWITGLPYVVDVANSVVISFGWMVNGDGDIQSHMNNA 131 Query: 126 AVALISLAIFLAFLWLSTKGLS-TLKVIGGLAGTAMFVMSLLFIVMAI-----GAPFIAK 179 L++ +F+ F+W ++ + +L+++ + G AMF+M++LF+ M I G+P + Sbjct: 132 WFGLLTAVVFIFFIWFQSRFQNKSLEIMSVIGGGAMFIMTVLFVGMTIVGLTQGSPIKTQ 191 Query: 180 DFHIATPDMGNIKTYIP-KFDFSYFTTISMLVFAVGGAEKISPYVNQTKNPAKEFPRGMF 238 F N++ ++P K D S+F T + +FA+ G+E +PY K+P+++FP+ + Sbjct: 192 PF--------NLQAFLPKKLDLSFFATFGLFIFAMNGSELAAPYTADMKHPSRDFPKSLK 243 Query: 239 LLAGMVGICAVLGSIAMGMIFSSGNLPNDLMANGAYAAFQILGQHFGVGNFLMIVYALTN 298 ++A M + G+ ++G+ F++ +LPNDL NG+Y AFQ +G+ FG+GN LM V+A+ Sbjct: 244 MIAVMTMFLTLFGTFSLGVYFNAHHLPNDLKMNGSYYAFQAIGKQFGLGNILMYVFAVVQ 303 Query: 299 GVGQIAALAFSIDAPLLILLADADPEFVSAWLRKKTNKGTLKNGYTLTGILVSIIILLPL 358 + +A LA +DA + L D F+ L K G NGY +T IL II+++ Sbjct: 304 CIYMLAQLAVILDASTRVFLGDMAKRFMPRQLSKTNAAGLPINGYWMTTILCGIIMVIAG 363 Query: 359 LGIGDMNELVKWLTNLNSVVMPMRYLWVFFAFIMLNRAVKHFQS-EYKFIKQKRLAMIAG 417 + +N++ WL NLN +V P ++F+AF+M+ R + + Y ++K R+ + G Sbjct: 364 F-LPQINDIFNWLLNLNGIVSPFSTCFLFWAFMMVRRHSDRYPTPSYTYLKNDRVGFLVG 422 Query: 418 AWCFLFTLIACVLGMVPKLDYAANPSAWWFQLASNILTPIVLILLGMLLPFIARREQRKT 477 W F T + ++G P +D A + W L I+ + +++LG L+P+IA+R QR+ Sbjct: 423 LWMFAITFLFALMGFWP-VDAAYGSALWTRSLVLYIVVTLGMVVLGFLMPWIAKR-QRER 480 Query: 478 NGL 480 +GL Sbjct: 481 DGL 483 Lambda K H 0.327 0.140 0.435 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: 802 Number of extensions: 43 Number of successful extensions: 5 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: 488 Length of database: 554 Length adjustment: 35 Effective length of query: 453 Effective length of database: 519 Effective search space: 235107 Effective search space used: 235107 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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