Align Inositol transport system permease protein (characterized)
to candidate WP_003940759.1 C1M55_RS10270 ABC transporter permease
Query= reanno::Phaeo:GFF716 (373 letters) >NCBI__GCF_002893965.1:WP_003940759.1 Length = 352 Score = 216 bits (551), Expect = 6e-61 Identities = 123/356 (34%), Positives = 189/356 (53%), Gaps = 26/356 (7%) Query: 11 DERIKTRSKFREAMIRPELGGIIGTITVFAMFLIFAGDSGMFNSQGVMNWSQISAQFMII 70 DER+K + + + ++RPE+G ++G I +F F I A + + +S S+ I+ Sbjct: 17 DERVKEQKRIQRLLLRPEMGSLVGAIAIFIFFCIVAAPFRTPEALATVLYS--SSTIGIM 74 Query: 71 AVGACLLMIAGEFDLSVGSMIGFAGMLIAIFSVTLGWPVWLAILVTFAIATAIGALNGFI 130 A LLMI GEFDLS G + + + ++ + L +W+ ++ ++ A+G NG++ Sbjct: 75 ACAVALLMIGGEFDLSAGVAVTTSSLAASMIAYNLHLNLWVGAILALVVSLAVGFFNGYL 134 Query: 131 VVRTGLPSFIVTLAFLFILRGFAIYLPQTIERKTIIGGVADAAEGDWLAALFGGKILTGL 190 V++T +PSF++TL+ +L G + + + + + V+D A D K+ Sbjct: 135 VMKTKIPSFLITLSSFLMLTGINLAVTKLVSGQVATPSVSDMAGFD-----SAKKVFASS 189 Query: 191 FQWFGDNGWIAVFERGTRKGQPVVEGLPMLIVWAILLVIIGHVILTKTRFGNWIFAAGGD 250 F FG + + + +VW +L I +L KT+ GNWIFA GG+ Sbjct: 190 FSVFGVS-------------------VKITVVWWLLFTAIATFVLFKTKIGNWIFAVGGN 230 Query: 251 AEAARNSGVPVNRVKILMFMFTAFCATVFATCQVMEFGGAGSDRGLLKEFEAIIAVVIGG 310 ++AR GVPV VKI +FM F A + F S +G+ EF IIA VIGG Sbjct: 231 QDSARAIGVPVTAVKIGLFMTVGFAAWFVGMHLLFSFNTVQSGQGVGNEFLYIIAAVIGG 290 Query: 311 ALLTGGYGSVLGAALGALIFGVVQQGLFFAGVESSLFRVFLGLILLFAVILNTYIR 366 LLTGGYG+ +GAA+GA IFG+ QG+ +AG F+ FLG +LLFAVI N R Sbjct: 291 CLLTGGYGTAIGAAIGAFIFGMTNQGIVYAGWNPDWFKFFLGAMLLFAVIANNAFR 346 Lambda K H 0.330 0.145 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: 485 Number of extensions: 33 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: 373 Length of database: 352 Length adjustment: 29 Effective length of query: 344 Effective length of database: 323 Effective search space: 111112 Effective search space used: 111112 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: 49 (23.5 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