Align N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS22735 HSERO_RS22735 sugar ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc02873 (419 letters) >FitnessBrowser__HerbieS:HSERO_RS22735 Length = 420 Score = 476 bits (1225), Expect = e-139 Identities = 224/402 (55%), Positives = 287/402 (71%), Gaps = 2/402 (0%) Query: 16 LGSAGLAQAQDATLTIESWRNDDLAIWQEKLIPAFEAKNPGIKVVFAPSAPTEYNAALNA 75 LGS A +Q TLTIESWR DDL +WQE LIPAF+ NPGI V F+P+APTEY+++L A Sbjct: 19 LGSLAAAPSQAGTLTIESWRVDDLPLWQEVLIPAFQRSNPGITVKFSPTAPTEYDSSLAA 78 Query: 76 KLDAGSAGDLITCRPFDASLELYNKKHLADLTGLSGMENFSDVAKSAWTTDDGKATFCVP 135 ++ G+AGDL+ CRPFD SL LYNK HL L G GME F+ AK+AW TDDG+ TFC+P Sbjct: 79 RMAGGTAGDLVACRPFDVSLSLYNKGHLEKLDGKPGMEFFAPAAKAAWQTDDGRDTFCMP 138 Query: 136 MASVIHGFIYNKDAFDQLGLSVPATEEEFFAVLEKIKADGNYIPMAMGTKDLWEAATMGY 195 MASVIHGF YN F +L L P TE EFF +L+ +KA+G Y P+ MGT + WE+ + + Sbjct: 139 MASVIHGFFYNTKIFKELNLEPPKTEAEFFKLLDTVKANGKYAPLVMGTAEQWESHQVLF 198 Query: 196 QNIGPNYWKGEEGRLALLKGEQKLTDEPWVEPFRVLAKWKDYLGDGFEAQTYPDSQNLFT 255 +IGPNYWKGEEGR AL+ G+ K TD +V + AK YL G AQTY DSQN+F Sbjct: 199 TSIGPNYWKGEEGRKALIAGKAKFTDPQFVAAWNYEAKLGKYLPKGASAQTYSDSQNMFA 258 Query: 256 LGRAAIYPAGSWEISGFNTQAEFKMGAFPPPVKKAGDTCYISDHNDIGIGLNAKSKNADA 315 LG+ A+YPAGSW+I+ FN + +F AFPPPV K GD CYISDHNDIG+G+N KSKN + Sbjct: 259 LGKGAVYPAGSWDIAYFNGKMDF--AAFPPPVPKNGDACYISDHNDIGMGINKKSKNKED 316 Query: 316 AKTFLTWVASPEFAEIYANALPGFFSLNSTAVKMSDPLAQEFVSWREKCKPTIRSTYQIL 375 A FL W+ S EFA++Y N + GFFSL++ + + DP+A++ + WR+ C TIR QIL Sbjct: 317 AYKFLAWLGSQEFADLYTNKVTGFFSLSNHLISVKDPIAKQMMGWRKNCASTIRVNSQIL 376 Query: 376 SRGTPNLENETWVMSANVINGTDTPEAAAKKLQDGLDSWFKP 417 +RGTP++ENE W ++A V+NG TP+ AA K+Q G W+KP Sbjct: 377 NRGTPSMENEMWNVNAQVLNGKMTPQDAAAKIQSGFAKWYKP 418 Lambda K H 0.315 0.132 0.401 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: 580 Number of extensions: 22 Number of successful extensions: 2 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: 419 Length of database: 420 Length adjustment: 32 Effective length of query: 387 Effective length of database: 388 Effective search space: 150156 Effective search space used: 150156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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