GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS03640 in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:D8IZC7
         (521 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS00275 BWI76_RS00275 ribose ABC
           transporter ATP-binding protein RbsA
          Length = 501

 Score =  418 bits (1074), Expect = e-121
 Identities = 222/493 (45%), Positives = 312/493 (63%), Gaps = 6/493 (1%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LLQ++GI K+F    ALS   L + PG + AL+GENGAGKST+MKVL+G++A D G +L 
Sbjct: 4   LLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLW 63

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            G+      P +S+ AGI +I+QEL + P +++A N+F+G E   R G ID   M +  D
Sbjct: 64  LGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
            +L +L   F +  L G LSI +QQ VEIA+ L   S+++IMDEPT AL++ ETE LF V
Sbjct: 124 KLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R L+ +G  I+YISHRM E++ + D VTV RDG F+ E     +D + +++MMVGR L 
Sbjct: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRKLE 243

Query: 246 EFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLL 305
           + Y     AP         ++V  L G  +   SF +R GE+LG AGL+GAGRTEL ++L
Sbjct: 244 DQYPRLDKAPGAVR-----LKVDNLCGSGVENISFILRQGEILGVAGLMGAGRTELMKVL 298

Query: 306 FGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASR 365
           +GA PRS G + L+GR V    P+  +  GI Y+ EDRK  GL L M+V  N ++     
Sbjct: 299 YGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358

Query: 366 HTR-LGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLI 424
            +R  G ++ +         I+  NVK    E  +G LSGGNQQKV +AR L   PKVLI
Sbjct: 359 FSRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLI 418

Query: 425 LDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELA 484
           LDEPTRGVD+ AK EIYQL+++  ++G++++++SSE+PEV+G+ DR++VM EG + GE  
Sbjct: 419 LDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFT 478

Query: 485 GAAITQENIMRLA 497
               TQE +M  A
Sbjct: 479 REQATQEVLMAAA 491



 Score =  106 bits (264), Expect = 2e-27
 Identities = 69/231 (29%), Positives = 116/231 (50%), Gaps = 14/231 (6%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81
           + ++   +R GEI  + G  GAG++ LMKVL G      G + LDGR V  R P    A 
Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327

Query: 82  GINLIYQE---------LAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTDAVLRQLG 132
           GI  I ++         ++V  N+S+ A  +         G + H   +      +R   
Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGG----GSLKHKDEQQAVSDFIRLFN 383

Query: 133 AGFGASDLA-GRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRD 191
               + + A G LS   QQ+V IAR L+ R +++I+DEPT  +     ++++ ++ + + 
Sbjct: 384 VKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKA 443

Query: 192 EGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242
           EGL+II +S  M EV  ++DR+ V+ +G   GE  R++   E ++   VG+
Sbjct: 444 EGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 494



 Score =  101 bits (252), Expect = 6e-26
 Identities = 68/247 (27%), Positives = 123/247 (49%), Gaps = 10/247 (4%)

Query: 267 VRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHID 326
           V+AL+G     AS +V  G V+   G  GAG++ + ++L G   R  G +L  G+    +
Sbjct: 17  VKALSG-----ASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSLLWLGKETTFN 71

Query: 327 QPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQ 386
            P+++  AGI  + ++     L  Q+ +A N  +       R G +  +++   A   + 
Sbjct: 72  GPKSSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKIDWKTMYAEADKLLA 127

Query: 387 RLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHR 446
           +LN++  + +  VG LS G+QQ V +A+ L    KV+I+DEPT  +       +++++  
Sbjct: 128 KLNLRF-NSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRE 186

Query: 447 LASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTA 506
           L SQG  +V IS  + E+  ICD V V R+G    E   A++ ++ ++ +     +    
Sbjct: 187 LKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRKLEDQY 246

Query: 507 PASHSSP 513
           P    +P
Sbjct: 247 PRLDKAP 253


Lambda     K      H
   0.320    0.135    0.378 

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: 644
Number of extensions: 25
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: 521
Length of database: 501
Length adjustment: 35
Effective length of query: 486
Effective length of database: 466
Effective search space:   226476
Effective search space used:   226476
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.

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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 preprint 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