Align TM1746, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_069331338.1 C8J29_RS19500 peptide ABC transporter substrate-binding protein
Query= TCDB::Q9X268 (642 letters) >NCBI__GCF_003046325.1:WP_069331338.1 Length = 529 Score = 162 bits (409), Expect = 5e-44 Identities = 115/368 (31%), Positives = 183/368 (49%), Gaps = 22/368 (5%) Query: 49 IFEGLFGYVPDPKSLGGVKVVPAVCESYTVSEDGLTYTFYLRKDKRWSNGDPVTAYDFEF 108 ++EGL V D ++ KVVP V ES+ +SEDGLTYTF LR D +WSNGDPV A DF F Sbjct: 57 LYEGLV--VQDAQA----KVVPGVAESWEISEDGLTYTFKLRDDAKWSNGDPVVAEDFVF 110 Query: 109 AWKRAASPETPTLPLWASPVQYIKNVYDCKSGAKPLDELGVKALDDYTLQVTLSRPMPSF 168 A +R +P T + +A+ + I N +G K +ELGV+A+D++TL+ TL+ P P F Sbjct: 111 ALRRIMTPATAAI--YANILYPIANAEAVATGGKQPEELGVEAVDEHTLKFTLNAPTPYF 168 Query: 169 INMLVLGGAMPLHRKTVQEHPEDWWKPEYFVGNGPYVIESFTPNYEIVLVRNKYYVGDFP 228 + +L ++P+HR TV+ ++ KP V NG Y + SF PN IV+ +N+++ Sbjct: 169 LELLTHQSSLPMHRATVEAEGSNFTKPGVMVTNGAYKLVSFAPNDRIVMEKNEHFHDAAN 228 Query: 229 GNVDR---IVLKAGGLGLQQYLAGEIDAVFITAVGDYVFALKNKQLSKELHEESGVQWVG 285 +DR + + L+++ A E+ T V A + L ELH + Sbjct: 229 VAIDRVEWVPFEDRSACLRRFEADEVQ--MCTDVPAEQMAYMRENLKDELHVAPYLGTYY 286 Query: 286 YEITRSLSPVFDDIRIRKALAMAIDKKVLTDIVLGGMAIPTHAYCSPD-SEIAEAVKGIP 344 + + D R+R+A++M +D+ + + V +P ++ P S E + Sbjct: 287 LPVKGADGSPLKDKRVRQAISMVLDRDFIAEEVWQETMLPGYSMVPPGISNYVETPPALD 346 Query: 345 YDPE-------QAKKLLAEAGYPNGKGFPKVKFYITGASDPVAEALVDQWKKVLGITFEI 397 Y E +AK LL EAG G ++ + + A+ D K + GI + Sbjct: 347 YADEDLLDREDKAKALLEEAGVAEGSLTVQLSYNSSENHRNTMTAIADMLKNI-GINATL 405 Query: 398 ENIESGQF 405 +E + Sbjct: 406 NEMEGTNY 413 Lambda K H 0.319 0.138 0.431 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: 812 Number of extensions: 39 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: 642 Length of database: 529 Length adjustment: 36 Effective length of query: 606 Effective length of database: 493 Effective search space: 298758 Effective search space used: 298758 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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