GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Klebsiella michiganensis M5al

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:B2SYR5
         (512 letters)



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

 Score =  401 bits (1031), Expect = e-116
 Identities = 216/495 (43%), Positives = 315/495 (63%), Gaps = 4/495 (0%)

Query: 1   MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60
           M A L+   I K FPGV+AL G S +V  G+V  L+GENGAGKST++K+L G Y  D+G 
Sbjct: 1   MEALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGS 60

Query: 61  VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKR 119
           ++  G E  F    SS  AGI +IHQEL  +P LT+AEN+ LG +  N  G ++ +    
Sbjct: 61  LLWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120

Query: 120 FVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVL 179
              + L  + +  +    +  LSI  +QMVEI K L   ++VI +DEPT +L+  ETE L
Sbjct: 121 EADKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180

Query: 180 FKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVG 239
           F+++R+L++  R ++YISHRM EI+E+CD  T+FRDG+ IA    +  +  D ++  MVG
Sbjct: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLDEDLLIEMMVG 239

Query: 240 REISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLV 299
           R++ D Y    +  G VR     + G  + +  SF +R+GEI+G  GL+GAGR+ELM ++
Sbjct: 240 RKLEDQYPRLDKAPGAVRLKVDNLCGSGV-ENISFILRQGEILGVAGLMGAGRTELMKVL 298

Query: 300 YGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRH 359
           YGA  +  G + LDG+ +  RS  + + +GIV   EDRK +G+V   +V EN++++  R+
Sbjct: 299 YGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358

Query: 360 YLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVV 419
           + R G  L  K E +    FI+L  +KTPS  Q I  LSGGNQQK  ++R L     KV+
Sbjct: 359 FSRGGGSLKHKDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP-KVL 417

Query: 420 ILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGEL 479
           ILDEPTRG+DVGAK EIY +I Q    G +I+++SSE+PEVLG+SDRI+VM +G + GE 
Sbjct: 418 ILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEF 477

Query: 480 TRKDATEQSVLSLAL 494
           TR+ AT++ +++ A+
Sbjct: 478 TREQATQEVLMAAAV 492


Lambda     K      H
   0.320    0.136    0.385 

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: 36
Number of successful extensions: 7
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: 512
Length of database: 501
Length adjustment: 34
Effective length of query: 478
Effective length of database: 467
Effective search space:   223226
Effective search space used:   223226
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