Align ABC transporter (characterized, see rationale)
to candidate 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 326 bits (835), Expect = 7e-94 Identities = 180/353 (50%), Positives = 231/353 (65%), Gaps = 9/353 (2%) Query: 1 MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60 M + L K+ G +++ V L IA GEF VFVGPSGCGKSTLLR+IAGL+ G + Sbjct: 1 MSGITLRGAVKRYGETQVVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEGSI 60 Query: 61 LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120 I R V L+P ERGV MVFQ+YALYPHM+V +N+ FGLK+ K ++ +V ++I Sbjct: 61 HIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAASEI 120 Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180 L+LD L RKPK LSGGQRQRVA+GRA+ R P++ LFDEPLSNLDA LRV+MR EIARLH Sbjct: 121 LKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240 +G+TMIYVTHDQVEAMTLADKIVVL GRVEQVG+P ELY P + FVAGF+GSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGAPLELYRDPDNVFVAGFIGSPAMN 240 Query: 241 FLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVVV 300 FL R++ + G+ LP + +G P+++G+RP+H++L+ G G +V Sbjct: 241 FLDGRIENDA------VHLAGLPPLPVPGAAGRSG-PVTVGVRPQHIALE--PGGDGYLV 291 Query: 301 TAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDAD 353 E LG +Y++L L G V L L D + LF+A+ Sbjct: 292 ELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPVGLSLAPDRVMLFEAE 344 Lambda K H 0.320 0.137 0.394 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: 356 Number of extensions: 10 Number of successful extensions: 2 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: 381 Length of database: 351 Length adjustment: 30 Effective length of query: 351 Effective length of database: 321 Effective search space: 112671 Effective search space used: 112671 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: 49 (23.5 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