Align ABC transporter related (characterized, see rationale)
to candidate SM_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Smeli:SM_b21344 Length = 497 Score = 420 bits (1080), Expect = e-122 Identities = 220/495 (44%), Positives = 326/495 (65%), Gaps = 2/495 (0%) Query: 3 LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62 ++L ++ I K + G+ AL SL + EV AL+G+NGAGKSTL+K++TGA +D G ++ Sbjct: 1 MLLSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVV 60 Query: 63 FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADAR 122 F GE F+ P ++Q GI+T+YQE+NL P +VA+N++L EPRR GLI + M A Sbjct: 61 FAGEGVSFSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAA 120 Query: 123 AVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182 AVL F L+IDV P++ +S A +Q++AIAR V A+++++DEPT+SLD +EV +LF Sbjct: 121 AVLRAFNLEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDT 180 Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242 + LK GV++VFI H L+++Y+I DR+T++R+G+ + A++P+ L+ MLG+ L Sbjct: 181 IRTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKELA 240 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 ++ + R V LS+ + ++ ++LTV +G+ GLAGLLGSGR+E N Sbjct: 241 AFEAIAKDADEGAQR--PVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTETAN 298 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 +FG D + G I G+ QP DAI+ GI L EDRK+DGII +SIREN+ LAL Sbjct: 299 LIFGADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLALL 358 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 ++ + RQ EI + +I L I D+PI++LSGGNQQKV+L RWL +P LL Sbjct: 359 PKLARAGIVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLL 418 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482 ++DEPTRGIDIGA +EI++L+R L DEG+ +L+ SSEL+EL+A +++V VL D +V L Sbjct: 419 IVDEPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVAVL 478 Query: 483 SGAELTSQHVMQAIA 497 EL+ + A+A Sbjct: 479 PRKELSEAALFAAMA 493 Lambda K H 0.319 0.136 0.377 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: 609 Number of extensions: 32 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: 499 Length of database: 497 Length adjustment: 34 Effective length of query: 465 Effective length of database: 463 Effective search space: 215295 Effective search space used: 215295 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