Align L-glutamine and L-histidine transporter (characterized)
to candidate WP_057508921.1 ABB28_RS12350 amino acid permease
Query= reanno::Korea:Ga0059261_1577 (470 letters) >NCBI__GCF_001431535.1:WP_057508921.1 Length = 474 Score = 303 bits (775), Expect = 1e-86 Identities = 172/466 (36%), Positives = 258/466 (55%), Gaps = 16/466 (3%) Query: 5 LFRTKRVKDAAEQAPEHRLAATLSWPHLVALGVGAIVGTGILTLIG-VGAGKAGPAVIMS 63 L+ TK A E A L TL L ALG+GA++G GI + G A AGPA+++S Sbjct: 5 LWATKHPHAAHEDANGLSLTRTLGPWGLTALGIGAVIGGGIFVITGQAAANHAGPAIMLS 64 Query: 64 FVIAGAICACAALAYAEMATMMPASGSAYAYSYAVLGEIIAWVVGWSLILEYSLVVSTVA 123 FV+A C ALAYAE A M+P SGSAY+Y+YA GE+ AW +GW L+LEY + S VA Sbjct: 65 FVLAAICCGFCALAYAEFAAMVPVSGSAYSYTYATFGELAAWFIGWMLVLEYGVSASAVA 124 Query: 124 VGWSGYAAPLL-HAWTGMPLELMAGP------HANGIVNLPAIFIIAVVAGLLCLGTKES 176 V W+GY LL H +P L++ P I N+PA ++ ++ L +G ++S Sbjct: 125 VSWTGYFLSLLSHFDIHLPAALVSAPLDGQLRPTGAIANVPAAILVLLLTWLCYVGIRKS 184 Query: 177 ATLNAALVVVKIIALAVFVAVALPYFNGANLEPFAPFGFAKTISPD--GVERGVMAAAAI 234 + +N A+V++K + + +AV Y + AN +PF P + P G+E GV+ AA+ Sbjct: 185 SAMNMAMVILKTGLIVLVIAVGWKYVDPANWQPFIP----ENTGPGQFGME-GVLRGAAM 239 Query: 235 IFFAFYGFDAISTAAEETKNPGRDLAIGIVGSMIACVAIYMLVAVAAVGATPFTHFANSP 294 +FFA+ GF+A+S AA+E+ P RD+ IG++ S++ C +Y+ +A G P+T Sbjct: 240 VFFAYIGFEAVSVAAQESHRPQRDMPIGMMLSLVICTLLYIAMAAVMTGLVPYTLLGTDE 299 Query: 295 EPLALILRDLGRPGFATFLAVSAIIALPTVLLGFLFGQSRIFFTMARDGMLPIGLAKV-S 353 + + + + A++ L +V+L + GQ RIF M RDG+LP K+ Sbjct: 300 PVVTAVAAHPSLGWLRVVVEIGALVGLSSVVLVMIIGQPRIFMIMGRDGLLPPLFTKIHP 359 Query: 354 KRGSPVRITLFTAAIVAVIAGLLPIDEIAALANAGTLAAFTAVAVCMMVLRVRAPDMPRM 413 K +P T+ T +A++A L P+D + L + GTL AF AV ++VLR PD+PR Sbjct: 360 KYRTPHINTVITGIGIALLAALFPLDVLGELTSMGTLIAFAAVCAGVLVLRRTQPDLPRP 419 Query: 414 FRTPLWWLVGAIAVLGCIYLFFSLPVKTQLWFLAWNALGVVIYFAY 459 FR WLV ++ VL C+ L ++ + W +G IYF Y Sbjct: 420 FRIRGAWLVCSLGVLSCMALLSAMTFHNWMLMGVWTVVGFAIYFGY 465 Lambda K H 0.327 0.140 0.426 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: 640 Number of extensions: 35 Number of successful extensions: 6 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: 470 Length of database: 474 Length adjustment: 33 Effective length of query: 437 Effective length of database: 441 Effective search space: 192717 Effective search space used: 192717 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