Align Inositol transport system ATP-binding protein (characterized)
to candidate Ac3H11_1109 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 278 bits (710), Expect = 4e-79 Identities = 170/494 (34%), Positives = 270/494 (54%), Gaps = 13/494 (2%) Query: 27 VNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKP 86 V I+K +P VVA + V L V PG + A++GENGAGKSTLMKII G +PD G + G+ Sbjct: 1 VGITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQA 60 Query: 87 IVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAELLA 146 + P A+ GIAM+ Q +L +++AEN+W+G ++ +L V R + A Sbjct: 61 VQVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLDKSLTLAEVTQRISAKA-----A 115 Query: 147 RLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADL 206 +++DP V LS+ E Q VEI +A+ + +LI+DEPTS +T + V LF ++ L Sbjct: 116 EYGLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKL 175 Query: 207 KSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRELSQLFP 266 S+G I+YI+HK++E+ A+ V R G G+ + SL +M+G E L Sbjct: 176 ASEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPAL-E 234 Query: 267 LRETPIGDLLLTVRDLTLDGVFK------DVSFDLHAGEILGIAGLMGSGRTNVAETIFG 320 R G +L V+ L+L + D+ F++ AGE++GIAG+ G+G+ + + G Sbjct: 235 HRAVQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSG 294 Query: 321 ITPSSS-GQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379 + I + G+ P G + E+R G P + + N+ + Sbjct: 295 EDQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTRKNAV 354 Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439 G+G+I+ AL+ ED+ ++ VK +LSGGN QK ++ R + NP+LLI+ Sbjct: 355 GGSGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIVS 414 Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499 +PT G+DVGA A+I I L G AV+++S EL E+ + DR+ V+ +G L ++ R+ Sbjct: 415 QPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQRA 474 Query: 500 EATQEKVMQLASGM 513 EAT E++ + SG+ Sbjct: 475 EATVERIGEWMSGL 488 Lambda K H 0.320 0.136 0.381 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: 548 Number of extensions: 25 Number of successful extensions: 7 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: 517 Length of database: 513 Length adjustment: 35 Effective length of query: 482 Effective length of database: 478 Effective search space: 230396 Effective search space used: 230396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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