Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_068005521.1 PsAD2_RS10155 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >NCBI__GCF_001623255.1:WP_068005521.1 Length = 515 Score = 259 bits (663), Expect = 1e-73 Identities = 164/511 (32%), Positives = 281/511 (54%), Gaps = 13/511 (2%) Query: 15 PQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQ 74 P+T LL + NI+K F +VA +V L + G ++AL+GENGAGK+TLM I+ G Y Sbjct: 2 PETETVHPLLSLQNITKIFGDLVANGNVNLDLHAGEIVALLGENGAGKTTLMNILFGHYV 61 Query: 75 PDAGEIRLR---GKPIVFE--TPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSL 129 D G + +R G + E P AA +AGI M+HQ L +++ ENI +G E L + Sbjct: 62 ADEGRVMVRTSSGTLVDLEPGAPQAALEAGIGMVHQHFTLAENLTGLENIVLGTESLFAR 121 Query: 130 HMVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTS 189 + + EL+ + +D + +V L++ ERQ VEI KA+ D+ IL++DEPT+ Sbjct: 122 KFSRSKARAKLQ-ELMQSSGLEVDLDLRVSKLAVGERQRVEILKALYRDARILVLDEPTA 180 Query: 190 AITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNS 249 +T +E LF+ + L ++G I++I+HKM EV +D VAV R G + + Sbjct: 181 VLTPQESDSLFNTLKLLAAKGMAIIFISHKMAEVLGASDRVAVLRGGRIVADLPTSQCDR 240 Query: 250 DSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLD---GVFKDVSFDLHAGEILGIAGL 306 L +MVG + Q+ G+ +L + ++ + ++V+ L GEI+G+AG+ Sbjct: 241 HKLAELMVGHAV-QMAEREPGNPGEEILVFKGVSAGEGRELIENVNLSLRKGEIIGLAGV 299 Query: 307 MGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLS 366 G+G++ +A+ + G+ ++G +TL + ++ ++ AI+ G A + EDR G+ +S Sbjct: 300 SGNGQSMLAKVLSGLEEPTAGAVTLGSQPLK-ANAAAAIQSGVARIPEDRHHDGIVGAMS 358 Query: 367 VLENMEMAVL--PHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKAL 424 V EN+ + + P Y G ++ +R ++ K ++ LSGGN QK + Sbjct: 359 VEENLVLEEIRKPAYQRFGLLRFNEIRKRAQEAIKAYDIRCSGPLAVSRLLSGGNIQKIV 418 Query: 425 LARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRV 484 LAR L P +++ +P+RG+DVGA A+++R + G V++IS +L E+ +SDR+ Sbjct: 419 LARTLDQEPAIVLAAQPSRGLDVGATADVHRRLQEARDRGAGVLLISEDLDELFQLSDRI 478 Query: 485 MVMHEGELMGTLDRSEATQEKVMQLASGMTA 515 V+H G + + E +++V + +G +A Sbjct: 479 AVIHRGHVSEPMASEELDKKQVGLMMAGHSA 509 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: 584 Number of extensions: 39 Number of successful extensions: 9 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: 515 Length adjustment: 35 Effective length of query: 482 Effective length of database: 480 Effective search space: 231360 Effective search space used: 231360 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 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