Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS27990 AZOBR_RS27990 ABC transporter permease
Query= uniprot:A0A166QFV1 (320 letters) >FitnessBrowser__azobra:AZOBR_RS27990 Length = 310 Score = 147 bits (370), Expect = 4e-40 Identities = 99/294 (33%), Positives = 155/294 (52%), Gaps = 12/294 (4%) Query: 22 QRRRVRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYLFHNGS 81 ++ R RA L P L+ L + P L SLT +L + G T F + L Sbjct: 19 EQTRRRAYLAGLLPALVVLGGITLLPGLFLLGVSLTPLSLVNPG--TVFDFSDPL----G 72 Query: 82 SWSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWAI 141 ++ +L D ++ N+V L+ + SVGL++ GL VALLLN++ +RA LIP + Sbjct: 73 NYRELLRDARFHNSVLLQLHLSATSVGLQLAAGLGVALLLNVRARFFEAIRAAFLIPMVL 132 Query: 142 PTIVSAKIWSWMLNDQFGIINHLMLSLGL-IDAPLAWTADADLSMWAVIIVDVWKTVPFV 200 P IV A IW + ++ L+ GL +D+ + D L++WA+ + + W+ PF Sbjct: 133 PPIVVALIWKILYTPDVSPLHRLLEEAGLPVDSLIT---DPTLAIWAIAVAETWQWFPFT 189 Query: 201 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 260 L++LA LQ++P + EAAR+DG + +VF + L L PAL+V +FR++DSL+ F +I Sbjct: 190 MLMVLATLQLIPDEPLEAARIDGANRRQVFRHIILAYLRPALVVCGLFRLIDSLKAFPLI 249 Query: 261 YVLTSNSSSTMS--MSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLG 312 YVLT+ T + + Y F GY SA + L+ V ++ L LG Sbjct: 250 YVLTNGGPGTATEVTNYYGFIEAFNFSYWGYASAIAVLMLGGVFAVSWLVGRLG 303 Lambda K H 0.329 0.140 0.443 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: 245 Number of extensions: 9 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: 320 Length of database: 310 Length adjustment: 27 Effective length of query: 293 Effective length of database: 283 Effective search space: 82919 Effective search space used: 82919 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