GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupA in Klebsiella michiganensis M5al

Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein

Query= TCDB::Q8DU37
         (510 letters)



>FitnessBrowser__Koxy:BWI76_RS27035
          Length = 513

 Score =  287 bits (735), Expect = 6e-82
 Identities = 173/489 (35%), Positives = 280/489 (57%), Gaps = 20/489 (4%)

Query: 5   VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTS--GSI 62
           ++EM+ ITK F    A D+++L L  GE+ +L GENG+GKSTLM +L G+    S  G I
Sbjct: 4   LLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63

Query: 63  KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEI 122
             +G  +       + + GI ++HQ   LV+  TV ENI LG E+ ++G+LD +      
Sbjct: 64  IFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLRC 123

Query: 123 KALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMT 182
           + L  +  LA+ P+ ++ D+ +G QQ VEI K L +   +LI DEPTA LT  E   L+ 
Sbjct: 124 EKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLN 183

Query: 183 IMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSV 242
           I++ L   G + I I+HKL+E+++++D + VIR G+ I T    G +  D+  MMVGR +
Sbjct: 184 IIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGREL 243

Query: 243 SFTIEKTPTKPKETILSIKDLVV--NENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300
           +           + IL +++L      NR I  +  +S  ++ GEI+GIAG+ G G++E 
Sbjct: 244 TALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGRTEA 303

Query: 301 VQAITGLRKIK-SGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAEN--L 357
           VQ + G+   +  G + I GQ VT  + ++     +  VPEDR +DG++  + + +N  L
Sbjct: 304 VQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKNITL 363

Query: 358 ALQTYYKAPLSHNGVLNYSKINEHGRHL-----MQEFDVRGANELIPAKGFSGGNQQKAI 412
           A    +  PL        S +++ G  L     +Q   ++ ++  +     SGGNQQKAI
Sbjct: 364 AALNQFTGPL--------SSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAI 415

Query: 413 IAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRI 472
           +AR +  +P +LI+ +PTRG+D+GA   I+K +     +G AV+++S EL E+L LSDR+
Sbjct: 416 LARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRV 475

Query: 473 AVIHDGQIQ 481
            V+H+G+++
Sbjct: 476 LVMHEGKLK 484



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 64/220 (29%), Positives = 105/220 (47%), Gaps = 8/220 (3%)

Query: 24  INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPT-SGSIKINGSAVTIDSPSKSAQLGI 82
           ++  LR+GEI  + G  GAG++  +  L G+      G I I+G  VTI +  ++   GI
Sbjct: 280 VSFSLRRGEILGIAGLVGAGRTEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGI 339

Query: 83  GMVHQHFM---LVEAFTVTENIILGNEVVKNGILD-LKKAGQEIKALSEKYGLAV---DP 135
            MV +      +V    V +NI L       G L  L  AG+++        L +    P
Sbjct: 340 AMVPEDRKKDGIVPVMAVGKNITLAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSP 399

Query: 136 NAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKSII 195
              I  +S G QQ+  + + L     ILI DEPT  +      E+  ++  LV++G ++I
Sbjct: 400 ELAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVI 459

Query: 196 LITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAE 235
           +I+ +L E+  ++DRV V+  GK    +   G T + + E
Sbjct: 460 VISSELPEVLGLSDRVLVMHEGKLKANLINQGLTQEQVME 499



 Score = 73.6 bits (179), Expect = 2e-17
 Identities = 60/236 (25%), Positives = 118/236 (50%), Gaps = 18/236 (7%)

Query: 271 IPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKI 330
           + AI  +SL + AGE++ + G +G+G+S L++ + G+      H + +G+ +    T   
Sbjct: 17  VKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYP----HGSYEGEIIFSGET--- 69

Query: 331 TELSVGHVPEDRHRDGLIL---ELTMAENLAL--QTYYKAPLSHNGVLNYSKINEHGRHL 385
             L  GH+  D  R G+ +   EL + ++L +    +  A +S +G+L+Y  +      L
Sbjct: 70  --LQPGHI-RDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLRCEKL 126

Query: 386 MQEFDVRGANELIPAKGFSG-GNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKR 444
           + + ++  + +     G  G G QQ   IA+ +++   LLI+ +PT  L       +   
Sbjct: 127 LAQVNLAISPDT--RVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLNI 184

Query: 445 LIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500
           +   ++ G A + +S +L+E+  +SD I VI DGQ  G    +  ++ ++  +M G
Sbjct: 185 IRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVG 240


Lambda     K      H
   0.315    0.135    0.363 

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: 567
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 510
Length of database: 513
Length adjustment: 35
Effective length of query: 475
Effective length of database: 478
Effective search space:   227050
Effective search space used:   227050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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