Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_011650501.1 RL_RS03915 carbohydrate ABC transporter permease
Query= uniprot:A8LLL4 (385 letters) >NCBI__GCF_000009265.1:WP_011650501.1 Length = 387 Score = 415 bits (1066), Expect = e-120 Identities = 219/380 (57%), Positives = 278/380 (73%), Gaps = 20/380 (5%) Query: 15 VQLSVVGLVVLWLLPTFGLFVSSFRTVEQISSSGWWKAMFPSEQNLTLRAADPDDFRMPQ 74 V L+V+ +V++WL+PT G+FVS+ R +QI SGWW A S Q +R PD + + Sbjct: 17 VHLAVLLIVIIWLIPTLGIFVSALRDKDQIVVSGWWTAFVGSTQTAAVRLGTPDQQKQ-E 75 Query: 75 GDLFVVKGNLFEDEGISEAEISVWGTSSRDVAAYTAGETADLGDGETITVQSNGAYVW-- 132 G +V+ GN+ E G + E+ +G + AA+ AGETADLGDGET+ + S+G+Y + Sbjct: 76 GASYVISGNVLE--GQTGREVKAFGNRVQQPAAFKAGETADLGDGETLQINSDGSYRYVK 133 Query: 133 --SGTDDQISGRGQRVFVTATTPPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATI 190 + + DQ R +R++ + + PPEFT NY +L SEG+ ++F N+LTVTIPATI Sbjct: 134 NAAFSPDQ---RPRRIYASVSAPPEFTMQNYNTVL----TSEGIGQSFINSLTVTIPATI 186 Query: 191 IPILVAAFAAYALAWMEFPGRALLIALIVGLLVVPLQLALIPLLTLHNAIGI-----GKG 245 IPIL+AAFAAYAL+WMEFPGR LLIAL+VGL+VVPLQ++LIPLL L+N IG K Sbjct: 187 IPILIAAFAAYALSWMEFPGRGLLIALVVGLIVVPLQMSLIPLLRLYNEIGNILGQPSKT 246 Query: 246 YLGTWLAHTGFGMPLAIYLLRNYMVGLPRDIIENAKVDGATDFQIFTKIVLPLSFPALAS 305 Y G WLAHT FGMPLAIYLLR Y+ GLP++IIE+A+VDGA+DF+IF +IVLPLSFPALAS Sbjct: 247 YPGIWLAHTAFGMPLAIYLLRAYIAGLPKEIIESARVDGASDFEIFVRIVLPLSFPALAS 306 Query: 306 FAIFQFLWTWNDLLVAKVFLIDATGQTTVMTNQIVELLGTRGGNWEILATAAFVSIAVPL 365 FAIFQFLW WNDLLVA VFL V+T + LLG+RGGNWEIL +AFV+I VPL Sbjct: 307 FAIFQFLWVWNDLLVAMVFL-GTDKDHIVLTGSLNALLGSRGGNWEILTASAFVTIIVPL 365 Query: 366 LVFFSMQRFLVRGLLAGSVK 385 LVFF +QR+LVRGLLAGSVK Sbjct: 366 LVFFGLQRYLVRGLLAGSVK 385 Lambda K H 0.323 0.138 0.419 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: 467 Number of extensions: 18 Number of successful extensions: 6 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: 385 Length of database: 387 Length adjustment: 30 Effective length of query: 355 Effective length of database: 357 Effective search space: 126735 Effective search space used: 126735 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 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