Align Amino-acid carrier protein, AlsT (characterized)
to candidate 5208581 Shew_1092 amino acid carrier protein (RefSeq)
Query= TCDB::Q45068 (465 letters) >FitnessBrowser__PV4:5208581 Length = 492 Score = 445 bits (1144), Expect = e-129 Identities = 226/458 (49%), Positives = 315/458 (68%), Gaps = 8/458 (1%) Query: 6 NSLINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGEKPEGNKGVSSMQ 64 +S IN + +W L Y+L+ G+ FT+R GFIQ R F ++V + E G+SS Q Sbjct: 10 DSTINAVNGMLWGSVLIYVLVAAGVLFTLRLGFIQLRMFGHGSKLVLQGREKTNGISSFQ 69 Query: 65 AFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRDGE 124 F S A+RVGTGN+ GVA+AI GG GAVFWMW++A +GMA++F+ESTLAQ+YKV+D + Sbjct: 70 VFCTSMAARVGTGNMAGVAVAITVGGAGAVFWMWLIALLGMATAFIESTLAQVYKVKDSD 129 Query: 125 -DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIVVA 183 +RGGPAYY+++GLG RW+G +F++L+ ++FG FNA Q NT+ AL+ AF ++K +V Sbjct: 130 GQYRGGPAYYMEQGLGKRWMGSLFSVLLIIAFGFAFNAAQANTMTDALNNAFGLDKTMVG 189 Query: 184 IVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKNAL 243 +V+ + A+II GGLK+V S+LIVPVMA Y+ IAL V++ N+ P +A IVK+A Sbjct: 190 LVIVAVAAYIISGGLKKVAKASELIVPVMAVAYLAIALIVLVMNLEQVPAALAYIVKSAF 249 Query: 244 GFEQVVGGGIGGIIVIGAQRGLFSNEAGMGSAPNAAATA--HVSHPAKQGFIQTLGVFFD 301 G+E+ GG +G ++ G RGLFSNEAGMGSA N AA+A + +HPA QGF+Q +GVF D Sbjct: 250 GWEEAAGGAMGAMMA-GIARGLFSNEAGMGSAANIAASASPNPNHPASQGFVQMIGVFVD 308 Query: 302 TFIICTSTAFIILLYSVTP---KGDGIQVTQAALNHHIGGWAPTFIAVAMFLFAFSSVVG 358 T +IC++TA IILL V + GI + Q AL + +GGWA F+A A+ LF FSS++ Sbjct: 309 TIVICSATAAIILLSGVLDAPGEQKGIGLLQLALTNEVGGWAAYFVAFAIILFCFSSIIA 368 Query: 359 NYYYGETNIEFIKTSKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALINLIVI 418 NY Y E+NI F+ SK L I+R V+AMV+ GS++ Q+VW+ AD+ MG+MAL+N+ I Sbjct: 369 NYSYAESNIMFLSRSKKVLYIFRALVLAMVMAGSVASLQLVWNFADVSMGLMALVNIAAI 428 Query: 419 ALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGLKNAE 456 +LS VA+ V KDY Q K G P F A + P L + Sbjct: 429 VMLSKVAFAVIKDYEVQLKAGKVPTFDAAHFPELNGLD 466 Lambda K H 0.327 0.142 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: 601 Number of extensions: 24 Number of successful extensions: 5 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: 465 Length of database: 492 Length adjustment: 34 Effective length of query: 431 Effective length of database: 458 Effective search space: 197398 Effective search space used: 197398 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 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