Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 379 bits (973), Expect = e-109 Identities = 202/493 (40%), Positives = 317/493 (64%), Gaps = 6/493 (1%) Query: 25 PYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGEL 84 PYL + K FPGV AL+D+ G V ALMGENGAGKSTL+KI++G Y P G + Sbjct: 6 PYL-SFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64 Query: 85 RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHREMHRC 144 + G+ ++F AAL AG+A+I+QEL+L+P M++AENI++G+ G I +R + Sbjct: 65 VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGG--IVNRSLLNY 122 Query: 145 TAQL-LERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHL 203 A L L+ L +++DP+ + LSI + QMVEIAKA++ ++ I+ DEPTS+++ +E+ +L Sbjct: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182 Query: 204 FSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIG-LQRADSMDGDSLISMMVG 262 F +I +L+ +G+ I+Y++H+M E+F+++D + VF+DG Y+ +D D+L+ MVG Sbjct: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242 Query: 263 RELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLHAGEILGIAGLMGSGRTNVAEAI 322 R++ ++ + + G+ + + ++ GV +S + +GEI+G+ GL+G+GR+ + + + Sbjct: 243 RDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 Query: 323 FGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-P 381 FG T G++ +D QP+ I P AI G L EDRK G+ P SV +N+ ++ Sbjct: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362 Query: 382 HYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILI 441 H G I + + L +KTP EQ I LSGGNQQKA+L RWL ++++ Sbjct: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422 Query: 442 LDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLD 501 LDEPTRGIDVGAK EIY +I LA++G+AV+ SS+LPEVLG++DR++VM EG++ G L Sbjct: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482 Query: 502 RSEATQERVMQLA 514 +A + + + LA Sbjct: 483 HEQADERQALSLA 495 Lambda K H 0.321 0.137 0.391 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: 647 Number of extensions: 23 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: 521 Length of database: 504 Length adjustment: 35 Effective length of query: 486 Effective length of database: 469 Effective search space: 227934 Effective search space used: 227934 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