Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate WP_005812351.1 DHAF_RS06640 amino acid permease
Query= TCDB::P40812 (497 letters) >NCBI__GCF_000021925.1:WP_005812351.1 Length = 452 Score = 387 bits (995), Expect = e-112 Identities = 184/425 (43%), Positives = 289/425 (68%), Gaps = 5/425 (1%) Query: 19 LNAHEEGYHKAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFIL 78 ++ E G H+ + NR +QMIA+GGAIGTGLF G+ A +++AGPA+ YLI G+ FFI+ Sbjct: 1 MSNQENGMHRGLKNRHIQMIALGGAIGTGLFYGSAATIELAGPAITFSYLIGGLVIFFIM 60 Query: 79 RALGELVLHRPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGA 138 R LGE+ + P SGSF +A ++ GE +++GW Y+ N+ + + ++TAV +Y+++W Sbjct: 61 RMLGEMAVDEPVSGSFSHFAYKYWGEFPGFLSGWNYWFNYIVVSMAELTAVGIYINFW-- 118 Query: 139 FGDVPQWVFALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFLGTGQPL 198 F D+P W+ AL L +V +N+I V F E EFWFA++KV+AI+ +V G + +G + Sbjct: 119 FPDIPHWLTALVCLVLVTLLNLISVGTFGEFEFWFAIVKVVAIIGMIVFGLFLIFSG--I 176 Query: 199 EGNATGFHLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAIN 258 G ATGF + +GGF P+G++ L + V+F+F IEL+G AGE +PQK +PKAIN Sbjct: 177 NGEATGFDNLWIHGGFIPNGMIGILFSLVPVMFSFGGIELIGITAGEADNPQKSIPKAIN 236 Query: 259 SVIWRIGLFYVGSVVLLVLLLPWNAYQAGQSPFVTFFSKLGVPYIGSIMNIVVLTAALSS 318 V+WRI +FYVG++ +L++L PWN A SPFV FSK+G+P +++NIVVLTAALS Sbjct: 237 QVMWRILIFYVGALSVLMVLYPWNQVGADGSPFVMIFSKIGIPAAATLLNIVVLTAALSV 296 Query: 319 LNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSRVF 378 NSG+Y GR+L S++M G+APK AK++++ +P AG+L + + +VGV LN+L+P ++F Sbjct: 297 YNSGVYSNGRMLYSLAMQGNAPKLFAKLNKRGIPVAGVLVSSGITLVGVILNFLLPGKIF 356 Query: 379 EIVLNFASLGIIASWAFIMVCQMRLRQA-IKEGKAADVSFKLPGAPFTSWLTLLFLLSVL 437 ++ A + + +W I++ ++ R+A I +G+ + FK P P+T++ FL+ ++ Sbjct: 357 TYLMAVAIIAAVITWTTIIIVNLKFRKAKIAQGEGDALHFKTPLHPYTNYFCAAFLVMIV 416 Query: 438 VLMAF 442 +LMAF Sbjct: 417 ILMAF 421 Lambda K H 0.328 0.140 0.434 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: 679 Number of extensions: 35 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: 497 Length of database: 452 Length adjustment: 33 Effective length of query: 464 Effective length of database: 419 Effective search space: 194416 Effective search space used: 194416 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: 51 (24.3 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