Align Amino-acid carrier protein, AlsT (characterized)
to candidate WP_086509070.1 BZY95_RS06045 alanine:cation symporter family protein
Query= TCDB::Q45068 (465 letters) >NCBI__GCF_002151265.1:WP_086509070.1 Length = 492 Score = 396 bits (1017), Expect = e-114 Identities = 209/473 (44%), Positives = 306/473 (64%), Gaps = 16/473 (3%) Query: 8 LINIPSDFIW-KYLFYILIGLGLFFTIRFGFIQFRYFIEMFRIVGE----KPEGNKGVSS 62 ++++ +D +W K L +LI +G+ FT+ F+QFRYF MFRI+G K + + +SS Sbjct: 1 MLDLINDLLWGKVLIALLIAVGVGFTLSSRFVQFRYFARMFRILGASQAFKRDKHGHLSS 60 Query: 63 MQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRD 122 QA +S A RVG GN+ GVA+AI GGPGA+FWMW+V +GMA+SF+E TLAQ YK Sbjct: 61 FQALLLSIAGRVGGGNIAGVAVAITLGGPGAIFWMWLVGLMGMATSFLECTLAQAYKTAQ 120 Query: 123 GED-FRGGPAYYIQKGLGARW--LGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNK 179 + +RGGPAYYI +GLG+RW L ++++L+ V+FG F A+Q+ +A + D AF + Sbjct: 121 PDGTYRGGPAYYIARGLGSRWKWLAALYSVLLLVTFGFGFTALQSYAVATSFDDAFGIPV 180 Query: 180 IVVAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIV 239 + I +A + IIFGG+KR+ V++++VPVMA Y+LIA V+ N+ P V IV Sbjct: 181 LYTGIGMAAVVGLIIFGGIKRIARVTEVLVPVMAVGYLLIAFVVLGMNLPRIPEVFLLIV 240 Query: 240 KNALGFEQVVGGGIGGIIVIGAQRGLFSNEAGMGSAPNAAATAHVSHPAKQGFIQTLGVF 299 +A G E VGGGIG I++G +RGLFSNEAG+GSAPN AA A+V HPA QG +Q VF Sbjct: 241 NSAFGLEPAVGGGIGAAIMMGVKRGLFSNEAGLGSAPNVAAVAYVPHPANQGVVQAFSVF 300 Query: 300 FDTFIICTSTAFIILL---YSVTPKGD--GIQVTQAALNHHIGGWAPTFIAVAMFLFAFS 354 DT IIC++TAFIILL Y D G+ +TQ +L H+G W +F++VA+ LF FS Sbjct: 301 IDTLIICSATAFIILLSGAYDPASGADIGGVALTQVSLADHVGEWGRSFVSVALLLFGFS 360 Query: 355 SVVGNYYYGETNIEFIKTSK-TWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMALI 413 +++ NYY GE ++ + T N++RIA++A+ +G+L+ V+ AD+ MG +AL Sbjct: 361 TILYNYYLGENSLNYFSDGNVTLFNLFRIAIVALCAWGALTDLGTVFAFADVTMGFLALA 420 Query: 414 NLIVIALLSNVAYKVYKDYAKQRKQGL-DPVFKAKNIPGLK-NAETWEDEKQE 464 NLI + +L ++ +D+ +Q + G+ PVF A+ L + WE E ++ Sbjct: 421 NLIALLMLFKPGLRLMRDFDEQIRAGIRHPVFDAQKFADLDIDPAAWEIEPED 473 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: 626 Number of extensions: 38 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: 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 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