Alignments for a candidate for mglA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Klebsiella michiganensis M5al

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate BWI76_RS00275 BWI76_RS00275 ribose ABC transporter ATP-binding protein RbsA

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__Koxy:BWI76_RS00275
          Length = 501

 Score =  426 bits (1096), Expect = e-124
 Identities = 220/496 (44%), Positives = 335/496 (67%), Gaps = 10/496 (2%)

Query: 11  EYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSI 70
           E LL+++GI+K+FPGVKAL   +LNV P  + AL+GENGAGKST++K L GIY +D+GS+
Sbjct: 2   EALLQLKGIDKAFPGVKALSGASLNVYPGRVMALVGENGAGKSTMMKVLTGIYARDAGSL 61

Query: 71  VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGR-YPTKGMFVDQDKMYQD 129
           ++ GKE  F+  K + E GI ++HQELNL+ Q ++ +N++LGR +  +   +D   MY +
Sbjct: 62  LWLGKETTFNGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121

Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
              +  +L++  + +  VG LS+   QM+EIAK  S+ +K++IMDEPT +LT+ E   LF
Sbjct: 122 ADKLLAKLNLRFNSQKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRS 249
            +IR+LK +G GIVYISH+M+EIF++CD++T+ RDGQ+IA + +  LD D +I MMVGR 
Sbjct: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLDEDLLIEMMVGRK 241

Query: 250 LNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309
           L  ++P  +  PG V L+V +L       + ++SF L +GEILG+AGL+GA RT++++ L
Sbjct: 242 LEDQYPRLDKAPGAVRLKVDNLCG---SGVENISFILRQGEILGVAGLMGAGRTELMKVL 298

Query: 310 FGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
           +G   +SSG++TL G+++   +  + + +G   ++E+R+  G+   + +  N  ++ +R 
Sbjct: 299 YGALPRSSGSVTLDGREVVARSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRY 358

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMR---VKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426
           +    G L +   K + Q V D +R   VKTP     IG LSGGNQQKV I R L+T+P+
Sbjct: 359 FSRGGGSLKH---KDEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPK 415

Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
           +L+LDEPTRG+DVGAK EIYQLI +   +G  II++SSEMPE+LG++DRI+VM  G + G
Sbjct: 416 VLILDEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGG 475

Query: 487 IVDTKTTTQNEILRLA 502
               +  TQ  ++  A
Sbjct: 476 EFTREQATQEVLMAAA 491



 Score = 93.6 bits (231), Expect = 1e-23
 Identities = 62/229 (27%), Positives = 112/229 (48%), Gaps = 11/229 (4%)

Query: 29  LDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQGKEVDFHSAKEALEN 88
           ++N++  +R   I  + G  GAG++ L+K L+G   + SGS+   G+EV   S ++ L N
Sbjct: 268 VENISFILRQGEILGVAGLMGAGRTELMKVLYGALPRSSGSVTLDGREVVARSPQDGLAN 327

Query: 89  GISMVHQELN---LVLQRSVMDNMWLG--RYPTKG----MFVDQDKMYQDTKAIFDELDI 139
           GI  + ++     LVL  SV +NM L   RY ++G       D+ +   D   +F+    
Sbjct: 328 GIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRGGGSLKHKDEQQAVSDFIRLFNVKTP 387

Query: 140 DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERG 199
            ++    +G LS    Q + IA+      K++I+DEPT  +       ++ +I + K  G
Sbjct: 388 SMEQA--IGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKAEG 445

Query: 200 CGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGR 248
             I+ +S +M E+  + D I ++ +G        E    + ++A  VG+
Sbjct: 446 LSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQEVLMAAAVGK 494


Lambda     K      H
   0.319    0.137    0.388 

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: 604
Number of extensions: 25
Number of successful extensions: 6
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: 506
Length of database: 501
Length adjustment: 34
Effective length of query: 472
Effective length of database: 467
Effective search space:   220424
Effective search space used:   220424
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 (21.7 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:

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