Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate H281DRAFT_01668 H281DRAFT_01668 gamma-aminobutyrate:proton symporter, AAT family
Query= uniprot:A0A0C4YRF7 (472 letters) >FitnessBrowser__Burk376:H281DRAFT_01668 Length = 459 Score = 293 bits (751), Expect = 6e-84 Identities = 161/447 (36%), Positives = 248/447 (55%), Gaps = 2/447 (0%) Query: 15 EEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRAL 74 ++ L + LK RHI MIA+GG IG GLF+G+G IA AGP +LSY IGGV + +M L Sbjct: 2 QDYSLKKSLKQRHITMIALGGVIGAGLFVGSGSIIATAGPAAILSYLIGGVMVTLVMFML 61 Query: 75 GELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVP 134 GE+ P SGSF+TYA ++G +AGFA GW YWF ++T E + +H + P +P Sbjct: 62 GEMASRNPDSGSFSTYANSYLGEWAGFAVGWLYWFKSMITITVEAILLGAILHDFLPWLP 121 Query: 135 QWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTA 194 AL L L N +V FGE E+W + KV TI+ +V+G A I FG+ P P Sbjct: 122 VPAGALFMLIALMATNAYSVRAFGEAEYWLSFAKVATIIVFMVLG-ASILFGLQPGIPAP 180 Query: 195 SFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWR 254 NL HGGFMP G V+ + +V+F+ G E+ V AGE++NP K + A V+ R Sbjct: 181 GLLNLTDHGGFMPNGISPVISGVMVVIFSLGGSEIAAVAAGESENPSKNVIRAIKSVILR 240 Query: 255 ILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGI 314 +++FYVG++ I++ +PW + SP+V +F G GAA + +V+ + S NS + Sbjct: 241 VMVFYVGSVSILILCMPWTDKANLKSPYVSLFSMAGFTGAAVAMKIVLFVSFMSVMNSFL 300 Query: 315 FSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTS 374 FS RML++L+Q G AP FGR ++K VP A+ + + ++++ +F+ + Sbjct: 301 FSNSRMLFSLSQRGHAPAMFGRTNAKGVPMNALVLCLVVCVSILGIHFLSGGDLFLMLAK 360 Query: 375 ISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLD 434 S + W I++AH R+ + +FR P +NW+ + ++AV + + Sbjct: 361 SSGAFVMIVWIFIIVAHFAMRRQTKHEQRDPASFRAWFYPVSNWVALLALVAVLGSQAFN 420 Query: 435 PGTRVALYVAPVWFALLGIGYRFTKSR 461 P +R + A V AL + + + + R Sbjct: 421 PESRFQFWFA-VSTALAIVAWYYVRRR 446 Score = 31.2 bits (69), Expect = 8e-05 Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 3/60 (5%) Query: 129 WFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVT 188 WF V W+ LA +AVL A +FWFA+ + IVA + FG T Sbjct: 397 WFYPVSNWVALLALVAVL---GSQAFNPESRFQFWFAVSTALAIVAWYYVRRRHPSFGQT 453 Lambda K H 0.328 0.142 0.445 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: 625 Number of extensions: 30 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: 472 Length of database: 459 Length adjustment: 33 Effective length of query: 439 Effective length of database: 426 Effective search space: 187014 Effective search space used: 187014 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 (21.8 bits) S2: 51 (24.3 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