Align MalF, component of Maltose/trehalose porter (characterized)
to candidate WP_003562044.1 RL_RS19645 sugar ABC transporter permease
Query= TCDB::O51924 (300 letters) >NCBI__GCF_000009265.1:WP_003562044.1 Length = 294 Score = 212 bits (539), Expect = 1e-59 Identities = 109/277 (39%), Positives = 177/277 (63%), Gaps = 3/277 (1%) Query: 23 YLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFWYSTFV 82 +L++LPLL V++ I P++ T +S E FVG+ NY +++S F + Sbjct: 11 WLLMLPLLVVMISVIGWPLIDTVGLSFTDAKLVGTEGNFVGIDNYAKMISGSNFQRTLVT 70 Query: 83 TVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSY 142 T F+ VSV+ E ++G+ AL+LN++ +GR LRA++++PWA+PT+++A W L+YN Y Sbjct: 71 TAWFAIVSVAAEMVIGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEY 130 Query: 143 GLFNWILSILGVSPV--NWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLYEA 200 G N L+ LG+ +WLG P +A A+++AD WK PL+ L+ LA LQA+P+D+ A Sbjct: 131 GALNAALTQLGLLEAYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAA 190 Query: 201 ALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSISLL 260 +L+DGA F RF+ + LP L L+VAL+LRTI+A +VFDII+V+T GGP +T ++S+L Sbjct: 191 SLVDGAGAFARFRFVILPYLAGPLMVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSIL 250 Query: 261 AF-NYYNLGDYGIGSAISILTFVLVLSFTIVYLKVGR 296 + ++ G G++++++ +LV Y + R Sbjct: 251 VYQEAFSFQRAGSGASLALIVTLLVTLLAAGYAALVR 287 Lambda K H 0.329 0.145 0.436 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: 281 Number of extensions: 12 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: 300 Length of database: 294 Length adjustment: 26 Effective length of query: 274 Effective length of database: 268 Effective search space: 73432 Effective search space used: 73432 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 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