Align Arabinose ABC transporter permease (characterized, see rationale)
to candidate BPHYT_RS01810 BPHYT_RS01810 sugar ABC transporter permease
Query= uniprot:A0A161GM94 (322 letters) >FitnessBrowser__BFirm:BPHYT_RS01810 Length = 319 Score = 200 bits (509), Expect = 3e-56 Identities = 126/310 (40%), Positives = 186/310 (60%), Gaps = 19/310 (6%) Query: 26 MLLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIA 85 +LLA + V + ++F S N+ S + + M + + +G DLSVG+V A Sbjct: 7 ILLALAALVVFGLVRYEHFGSAYNITSFWRYNSMFALISVGMAFVIITGGIDLSVGTVAA 66 Query: 86 CAGVVAAVVMRDTNSVFLGISAALV---MGLIVGLINGIVIAKLRVNALITTLATMQIVR 142 A VVAA+ SV+ G A L GL VG++NG++I +L++ I TLAT Sbjct: 67 LASVVAALT-----SVYGGWVAVLAGCGAGLAVGVLNGLIITRLKILPFIVTLATSLGAH 121 Query: 143 GLAYIFANGKAVGVSQESFFV-FGNGQMFGVPVPILITIVCFLFFGWL-LNYTTYGRNTM 200 G+A + AV ++ ES F FG G +FG+P+P ++ +V + GWL L T +GR+++ Sbjct: 122 GVALLLGKNDAVSIAAESNFGNFGQGDLFGLPIPGIVAVVAAV-AGWLALRSTRFGRHSL 180 Query: 201 AIGGNQEAALLAGVNVDRTKIIIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISA 260 AIGG++EAA L G+NVDRT ++ +AV G++ +AGVILA++ +GQP G G+EL ISA Sbjct: 181 AIGGSEEAARLMGLNVDRTLVMAYAVSGLLAGMAGVILAAQFGAGQPNEGVGWELFAISA 240 Query: 261 CVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKN------IDTFYQYVIRGSILLLAV 314 VLGG L+GG G I IAGVL+L ++ N +N +N + ++Q VIRG LLL + Sbjct: 241 VVLGGTLLTGGEGSIAMTIAGVLLLGLVFNLLNFENGLGFISLSAYWQSVIRGVFLLLVI 300 Query: 315 VIDR--LKQR 322 V+ LKQR Sbjct: 301 VLQARVLKQR 310 Lambda K H 0.330 0.144 0.420 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: 288 Number of extensions: 18 Number of successful extensions: 3 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: 322 Length of database: 319 Length adjustment: 28 Effective length of query: 294 Effective length of database: 291 Effective search space: 85554 Effective search space used: 85554 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 (21.8 bits) S2: 48 (23.1 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