Align Sodium/proton-dependent alanine carrier protein (characterized)
to candidate Echvi_3279 Echvi_3279 amino acid carrier protein
Query= SwissProt::P30145 (445 letters) >FitnessBrowser__Cola:Echvi_3279 Length = 473 Score = 482 bits (1240), Expect = e-140 Identities = 248/432 (57%), Positives = 307/432 (71%), Gaps = 2/432 (0%) Query: 1 MIRLVTMGKSSEAGVSSFQALTMSLSGRIGVGNVAGTATGIAYGGPGAVFWMWVITFIGA 60 M RL+ G+SSE GVSSFQA +++SGR+G GN+AG A IA GGPGA+FWMWVI F+G Sbjct: 43 MFRLLFRGESSEKGVSSFQAFAIAISGRVGTGNIAGVAMAIAMGGPGAIFWMWVIAFLGG 102 Query: 61 ATAYVESTWRKFIKRNKTDNTVAVRRSTLKKALAGNGLRCSRA-AIILSMAVLMPGIQAN 119 A+A+VEST + K ++K L A A I+SM +LMPG+Q+N Sbjct: 103 ASAFVESTLGQVYKEVNEGQYRGGPAYYIEKGLGVKWYAMLFAFATIISMTLLMPGVQSN 162 Query: 120 SIADSFSNAFGIPKLVTGIFVIAVLGFTIFGGVKRIAKTAEIVVPFMAVGYLFVAIAIIA 179 SIA S NAFG+P TG+ + LG I GGVKRI+K AE+VVPFMA Y+ +A+ II Sbjct: 163 SIALSVQNAFGVPVEYTGMVITFFLGLIIIGGVKRISKVAEVVVPFMAAAYILMAMVIIG 222 Query: 180 ANIEKVPDVFGLIFKSAFGADQVFGGILGSAVMWGVKRGLYANEAGQGTGAHPAAAAEVS 239 +NI +VP V LI KSAF + F G+ G A+ WGVKRG+Y+NEAGQGT H AAAAEVS Sbjct: 223 SNITEVPAVLTLIVKSAFNLEAAFSGVFGMAIAWGVKRGIYSNEAGQGTAPHAAAAAEVS 282 Query: 240 HPAKQGLVQAFSIYLDVFLVVTATALMILFTGQYNVINEKTGETIVEHLKGVEPGAGYTQ 299 HPAKQGLVQAFS+Y+D V TATALMILFTGQ+NV+N + G I E+L GVE G YTQ Sbjct: 283 HPAKQGLVQAFSVYVDTLFVCTATALMILFTGQFNVVNPE-GGFIKENLPGVEVGPEYTQ 341 Query: 300 AAVDTLFPGFGSAFIAIALFFFAFTTMYAYYYIAETNLAYLVRSEKRGTAFFALKLVFLA 359 AV T FP GS F+AI+L FFAFTT+ AYYYIAETNL+YL R + R + +AL+++ LA Sbjct: 342 YAVATHFPDLGSGFVAISLLFFAFTTIMAYYYIAETNLSYLNRFKHRAWSLWALRVMILA 401 Query: 360 ATFYGTVKTATTAWAMGDIGLGIMVWLNLIAILLLFKPAYMALKDYEEQLKQGKDPEFNA 419 ATFYGT+KTA AW +GDIG+G+M WLN+IAI+LL KPA DY +QLK GKDP F A Sbjct: 402 ATFYGTIKTAKVAWMLGDIGVGLMAWLNVIAIVLLRKPAMKTFNDYRKQLKAGKDPVFKA 461 Query: 420 SKYGIKNAKFWE 431 + G+ NA FW+ Sbjct: 462 KEAGVDNADFWK 473 Lambda K H 0.324 0.137 0.407 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: 637 Number of extensions: 37 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: 445 Length of database: 473 Length adjustment: 33 Effective length of query: 412 Effective length of database: 440 Effective search space: 181280 Effective search space used: 181280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 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