GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruK in Herbaspirillum seropedicae SmR1

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS03640 HSERO_RS03640 D-ribose
           transporter ATP-binding protein
          Length = 502

 Score =  355 bits (910), Expect = e-102
 Identities = 194/482 (40%), Positives = 293/482 (60%), Gaps = 13/482 (2%)

Query: 4   KNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGS 63
           + P++ M+GI   F    AL  + LT+ PGE+HALMGENGAGKST++K L+GV+  + G 
Sbjct: 7   QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 66

Query: 64  IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFG-IDWKKTHE 122
           I++DG+P        ++ AGI  +YQE+ +  N+SV  NV +G E R   G ID      
Sbjct: 67  ILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRS 126

Query: 123 AAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182
                L Q+G            +SIA QQ V IARA+V  ++++I+DEPT++L   E   
Sbjct: 127 RTDAVLRQLGA-GFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQ 185

Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242
           LF ++R++RD G+AI+++SH + ++Y + DR+T+LR+G F+ E++  +   + ++ MM+G
Sbjct: 186 LFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 245

Query: 243 KSAAELSQIGAKKARREITPGEKP----IVDVKGLGKKGTINPVDVDIYKGEVVGFAGLL 298
           +S +E  Q       + I P +      ++ V+ L   G I P   D+  GEV+GFAGL+
Sbjct: 246 RSLSEFYQ------HQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLV 298

Query: 299 GSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTV 358
           G+GRTEL RLL+GAD    G   L G+ V+I  P  A++  IAY  E+R+ +G+   + V
Sbjct: 299 GAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAV 358

Query: 359 RQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418
             N  + + +       +  +    +    ++ LNV+ A P+ PV  LSGGNQQKVL+ R
Sbjct: 359 AANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLAR 418

Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478
           WL   P++LILDEPTRG+DI AK+EI Q+V  LASQG+ VV ISSEL EV+ + D + V+
Sbjct: 419 WLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVM 478

Query: 479 KD 480
           ++
Sbjct: 479 RE 480



 Score = 86.7 bits (213), Expect = 2e-21
 Identities = 55/201 (27%), Positives = 100/201 (49%), Gaps = 9/201 (4%)

Query: 33  GEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIATVYQE-- 90
           GEV    G  GAG++ + + L G    + G I+++G+P   +    A  AGIA V ++  
Sbjct: 289 GEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRK 348

Query: 91  -----VNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDPHTPLSSI 145
                + +    +   NV   H + G   +  +     A+  + ++ ++   P TP+  +
Sbjct: 349 GQGLFLQMAVAANATMNVASRHTRLGL--VRSRSLGGVARAAIQRLNVKVAHPETPVGKL 406

Query: 146 SIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLD 205
           S   QQ V +AR + I  KVLILDEPT  +D     +++ ++ ++   GVA++ +S  L 
Sbjct: 407 SGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELP 466

Query: 206 QIYEITDRLTILRNGQFIKEV 226
           ++  I DR+ ++R G    E+
Sbjct: 467 EVIGICDRVLVMREGMITGEL 487



 Score = 75.9 bits (185), Expect = 3e-18
 Identities = 61/244 (25%), Positives = 109/244 (44%), Gaps = 19/244 (7%)

Query: 264 EKPIVDVKGLGKKG----TINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGT 319
           + P++ ++G+ K       ++ + + I  GE+    G  G+G++ L ++L G   PD G 
Sbjct: 7   QTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGE 66

Query: 320 YTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGM-----FK 374
             L+G+ V + DP  +    I           I  +L V  NI +A     G        
Sbjct: 67  ILLDGRPVALRDPGASRAAGINL---------IYQELAVAPNISVAANVFMGSELRTRLG 117

Query: 375 PIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTR 434
            I      +  D  +++L       D   + LS   QQ+V I R L     ++I+DEPT 
Sbjct: 118 LIDHAAMRSRTDAVLRQLGAGFGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTA 176

Query: 435 GIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVS 494
            +      ++  VV  L  +G+ +++IS  + EV  L+D + VL+D   + E+  D+  S
Sbjct: 177 ALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS 236

Query: 495 QATI 498
           +  +
Sbjct: 237 ERIV 240


Lambda     K      H
   0.316    0.135    0.376 

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: 606
Number of extensions: 24
Number of successful extensions: 7
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: 513
Length of database: 502
Length adjustment: 34
Effective length of query: 479
Effective length of database: 468
Effective search space:   224172
Effective search space used:   224172
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: 41 (21.6 bits)
S2: 52 (24.6 bits)

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

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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