Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= TCDB::P48245 (273 letters) >FitnessBrowser__Miya:8502073 Length = 596 Score = 109 bits (272), Expect = 2e-28 Identities = 68/207 (32%), Positives = 120/207 (57%), Gaps = 11/207 (5%) Query: 27 LPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFAY 86 L GL +L AV ++ ++ +G A+G+GR S R+ R C + IE R P++I++ + Y Sbjct: 387 LGGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIRGNPLIIVIFWVY 446 Query: 87 QMFAQYNIVPSSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQT 146 F + ++ F + + LT + G+ IAEI+R+GI ++P GQ EAA + G++ Q Sbjct: 447 --FFIPVMFGTTLNVFWSATWALTAFTGAYIAEIVRTGIQNIPAGQVEAAYSTGLTYLQA 504 Query: 147 TWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEV--VRSGIQSASVNRNYLAALF 204 I+LPQA+ M+PA++ Q + KD++L + +G +E+ V GI NR + + Sbjct: 505 MRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLELTFVAQGIN----NRLMIHPME 560 Query: 205 V---VALIMIVLNFSLTALASRIERQL 228 + VA + + +S++ A+R+ER+L Sbjct: 561 IYGTVAFLYFICCYSMSVFAARLERRL 587 Score = 108 bits (270), Expect = 3e-28 Identities = 75/220 (34%), Positives = 117/220 (53%), Gaps = 14/220 (6%) Query: 26 ILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFRAIPVLILMIFA 85 IL GL T++ ++ S LAL++GT LGL R+S R LR +IE FR P+LI + F Sbjct: 57 ILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLRVTATCVIEFFRNTPLLIQLFFW 116 Query: 86 YQMFAQYNIVP--------SSQLAFAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAI 137 Y FA I+P S Q F GL++Y S +AE++R+G+ S+PKG EAA Sbjct: 117 Y--FAFPAILPDNAREALFSIQFEFWCATIGLSIYTASFMAEVIRAGLQSIPKGLLEAAY 174 Query: 138 ALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGYQIGYIEVVRSGIQSASVN- 196 + G+S Q +I+LP A A++P L S+ + +K+S+L +G E+ Q S+ Sbjct: 175 SSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKNSSLAMVVGVAELTWHAQQVESLTF 234 Query: 197 ---RNYLAALFVVALIMIVLNFSLTALASRIERQLRAGRA 233 AA + + ++++F L + R+ GR+ Sbjct: 235 KGFEATSAATVLYLSLSLIISFILNGVNGRMRLDTAPGRS 274 Lambda K H 0.323 0.136 0.395 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: 369 Number of extensions: 27 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 273 Length of database: 596 Length adjustment: 31 Effective length of query: 242 Effective length of database: 565 Effective search space: 136730 Effective search space used: 136730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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