Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Klebsiella michiganensis M5al

Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BWI76_RS19640 BWI76_RS19640 galactose/methyl galactoside ABC transporter ATP-binding protein MglA

Query= TCDB::Q9X051
         (523 letters)



>FitnessBrowser__Koxy:BWI76_RS19640
          Length = 506

 Score =  414 bits (1063), Expect = e-120
 Identities = 213/507 (42%), Positives = 330/507 (65%), Gaps = 10/507 (1%)

Query: 4   NTEKEREVLLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP 63
           N+E+  E LLE  NI K+FPGV A++NV L++    + AL+GENGAGKSTL+K L G+Y 
Sbjct: 5   NSERSGEYLLEMTNINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQ 64

Query: 64  DYEGQIFLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGV-IE 122
              G I  +G+E+ F + +EA ENGI+++ QEL+LV   S  +N++L R P    GV ++
Sbjct: 65  KDSGSILFQGQEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GVFVD 122

Query: 123 YQKMFEQASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGK 182
             KM+     +F +L ++IDP+ +V  LS SQ QM+ IAKA S +AKI+IMDEPTS++ +
Sbjct: 123 QDKMYRDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182

Query: 183 RETEQLFNIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLV 242
           +E   LF IIR LK  G  ++YISH++EEIF++ D + ++RDG+ +   P+E  D DK++
Sbjct: 183 KEVNHLFKIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKII 242

Query: 243 RLMVGRSIDQFFIKERATITDEIFRVEGIKLWSLDRKKLLVDDVSFYVRKGEVLGIYGLV 302
            +MVGRS++Q F  +     + I  V  +       ++  + D+SF + KGE+LGI GLV
Sbjct: 243 AMMVGRSLNQRFPNKENKPGEVILEVRNL----TSLRQPSIRDISFDLHKGEILGIAGLV 298

Query: 303 GAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMS 362
           GA RT+++E +FG    +  G + + GK+I  HS  +A+ +G  LV E+R++ G+   + 
Sbjct: 299 GAKRTDIVETLFGIRE-KAGGTIRLHGKKINNHSANEAINHGFALVTEERRSTGIYAYLD 357

Query: 363 VLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKV 422
           +  N  + ++  K    K GL+D+   K   +  I+ + +KTP  +  + +LSGGNQQKV
Sbjct: 358 IGFNSLISNI--KKYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGQHTQIGSLSGGNQQKV 415

Query: 423 VLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDR 482
           ++ +WL  +P++L+LDEPTRGIDV AK EIY+LI+E+A    G++++SSE+PE+L ++DR
Sbjct: 416 IIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKDKGIIIISSEMPELLGITDR 475

Query: 483 ILVMSEGRKTAEFLREEVTEEDLLKAA 509
           ILVMS G        +  T+ ++L+ A
Sbjct: 476 ILVMSNGLVAGIVETKTTTQNEILRLA 502



 Score = 98.6 bits (244), Expect = 5e-25
 Identities = 62/240 (25%), Positives = 122/240 (50%), Gaps = 10/240 (4%)

Query: 283 VDDVSFYVRKGEVLGIYGLVGAGRTELLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVK 342
           +D+V+  VR   +  + G  GAG++ LL+ +FG +  +  G +   G+EI  HS ++A++
Sbjct: 29  LDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQ-KDSGSILFQGQEIDFHSAKEALE 87

Query: 343 NGIGLVPEDRKTAGLILQMSVLHNITLPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNI 402
           NGI +V ++     L+LQ SV+ N+ L     K +      +D        ++  ++L+I
Sbjct: 88  NGISMVHQE---LNLVLQRSVMDNMWLGRYPTKGV-----FVDQDKMYRDTKAIFDELDI 139

Query: 403 KTPSPYQIVENLSGGNQQKVVLAKWLAIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVS 462
               P   V  LS    Q + +AK  +   K++++DEPT  +     + ++K+I ++   
Sbjct: 140 DI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFKIIRKLKER 198

Query: 463 GMGVVMVSSELPEILAMSDRILVMSEGRKTAEFLREEVTEEDLLKAAIPRSVKVETTQRE 522
           G G+V +S ++ EI  + D I ++ +G+  A    E +  + ++   + RS+      +E
Sbjct: 199 GCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLNQRFPNKE 258


Lambda     K      H
   0.317    0.137    0.372 

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: 600
Number of extensions: 35
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 523
Length of database: 506
Length adjustment: 35
Effective length of query: 488
Effective length of database: 471
Effective search space:   229848
Effective search space used:   229848
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources