Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate HSERO_RS05320 HSERO_RS05320 ribonucleotide-diphosphate reductase subunit alpha
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__HerbieS:HSERO_RS05320 Length = 502 Score = 353 bits (905), Expect = e-101 Identities = 195/493 (39%), Positives = 294/493 (59%), Gaps = 6/493 (1%) Query: 8 LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67 L GI K F V L + + AG+VHAL+GENGAGKSTL+KIL G P G + I+ Sbjct: 2 LQLTGIKKNFGPVTVLRGVDLEVRAGEVHALLGENGAGKSTLMKILCGIVRPDAGEIRID 61 Query: 68 GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYEAGL 126 GQ F AA+ GV +++QE L+P + +N++L +L + G + R+ + A Sbjct: 62 GQPCRFDSYRAAIAGGVGVVFQEFSLIPYLDAVDNMFLARELRSRWGWLQRAAMRRRAQE 121 Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186 + LG+ I D P+ LS+ Q Q VEIAKALA +A+I+ DEPT++L+ E+++LF V+ Sbjct: 122 IIGQLGVAIPLDVPVCKLSVAQQQFVEIAKALALDARILVLDEPTATLTPAEVEHLFAVM 181 Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246 R LR +G I+++SH +EEIF + D ITV +DG YV T + VD LV+ MVGR I Sbjct: 182 RSLRAQGVAIIFISHHLEEIFEICDRITVLRDGAYVATCATAE-VDQARLVEMMVGRRIE 240 Query: 247 DIYGWQPRSYGEER----LRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302 + + +P GE L + A++ +R GEI+G GLVG+GR+E + M Sbjct: 241 NCFPPKPAKGGEGEGEVVLEVHALQLRRQAPVSQFQLRRGEILGFAGLVGSGRTETVLAM 300 Query: 303 FGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRK 362 G + ++ + P+ P+ A+ AG+ L PE RK +G+I S+ N++++ K Sbjct: 301 LGAHAALSCKLSMHGVPLRFADPAQALQAGIGLLPESRKEQGLITSFSILHNVSLNNYGK 360 Query: 363 HVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVIL 422 + LGG ++ E+ + ++ + +K PGA+ + LSGGNQQK ++ RW++ MKV++ Sbjct: 361 YRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVRVDTLSGGNQQKVVIARWINHAMKVLI 420 Query: 423 LDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELL 482 DEPTRGIDVGAK EIY ++ AQG ++L SS+LPEV+G+ADR+ V R G I L Sbjct: 421 FDEPTRGIDVGAKSEIYQLMREFTAQGYSILMISSELPEVVGMADRVCVFRGGGIVATLE 480 Query: 483 HEQADERQALSLA 495 E + + ++ A Sbjct: 481 GEAVNAEEIMTHA 493 Score = 75.5 bits (184), Expect = 4e-18 Identities = 57/227 (25%), Positives = 103/227 (45%), Gaps = 15/227 (6%) Query: 28 FDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVAII 87 F G++ G G+G++ + + G +A + + ++G + F+D AL AG+ ++ Sbjct: 275 FQLRRGEILGFAGLVGSGRTETVLAMLGAHAALSCKLSMHGVPLRFADPAQALQAGIGLL 334 Query: 88 YQ---ELHLVPEMTVAENIYLGQLP--HKGGIV---NRSLLNYEAGLQ---LKHLGMDID 136 + E L+ ++ N+ L GG+ R EA +Q +K G + Sbjct: 335 PESRKEQGLITSFSILHNVSLNNYGKYRLGGLFLDRRREQQATEAAMQRVRVKAPGAQVR 394 Query: 137 PDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVI 196 DT LS G Q V IA+ + K++ FDEPT + +++++RE +G I Sbjct: 395 VDT----LSGGNQQKVVIARWINHAMKVLIFDEPTRGIDVGAKSEIYQLMREFTAQGYSI 450 Query: 197 LYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243 L +S + E+ ++D + VF+ G V T + + A GR Sbjct: 451 LMISSELPEVVGMADRVCVFRGGGIVATLEGEAVNAEEIMTHATTGR 497 Lambda K H 0.319 0.136 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: 670 Number of extensions: 40 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 504 Length of database: 502 Length adjustment: 34 Effective length of query: 470 Effective length of database: 468 Effective search space: 219960 Effective search space used: 219960 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 (21.7 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