GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS00275
          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:

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