Alignments for a candidate for mglA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Dyella japonica UNC79MFTsu3.2

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  390 bits (1003), Expect = e-113
 Identities = 222/500 (44%), Positives = 311/500 (62%), Gaps = 11/500 (2%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS--GSI 70
           L EMRGI KSF GVKALD ++L +R      L GENGAGKSTL+K L G+Y   S  G I
Sbjct: 7   LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66

Query: 71  VFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYQD 129
           ++QG+ +   S +++   GI ++HQEL LV Q SV +N++LG   T+ G  +D D MY  
Sbjct: 67  LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMYAK 126

Query: 130 TKAIFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHL 188
             A+  EL + D++             Q+ EIAKA +  AK++I+DEPTSSLT  E   L
Sbjct: 127 ADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETEVL 186

Query: 189 FTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGR 248
             I+  LK RG   +YISHK++E+ ++CD + ++RDG+ IATQP+  LD+D +I +MVGR
Sbjct: 187 LGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLMVGR 246

Query: 249 SLNQRFPDKENKPGDVILEVRHLTSL-----RQPSIRDVSFDLHKGEILGIAGLVGAKRT 303
            L   +P  E+  G+VI E RH T L     ++  + DVSF L +GEILGIAGLVGA RT
Sbjct: 247 KLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRT 306

Query: 304 DIVETLFG-IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNS 362
           ++V  +FG    KSS  + L G+ +   +  +AI  G  +V E+R+  GI   L +G N 
Sbjct: 307 ELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNI 366

Query: 363 LISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLL 422
            ++ + +Y +  G +D  R     +  I   RVKT      I  LSGGNQQK ++ + LL
Sbjct: 367 TLATLDHYAH-AGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLL 425

Query: 423 TQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482
            +P++L+LDEPTRG+DVGAK EIY+LI ELA +G  I+++SSEMPE+LG+ DR+LVM  G
Sbjct: 426 ARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEG 485

Query: 483 LVSGIVDTKTTTQNEILRLA 502
            + G    +  TQ ++L  A
Sbjct: 486 RLRGDFPNQGLTQEQVLAAA 505



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 62/250 (24%), Positives = 114/250 (45%), Gaps = 10/250 (4%)

Query: 10  GEYLLEMRG---INKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQ-K 65
           GE + E R    ++   P  K +D+V+  +R   I  + G  GAG++ L+  +FG Y  K
Sbjct: 260 GEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGK 319

Query: 66  DSGSIVFQGKEVDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLG---RYPTKGM 119
            S  +  +G+ +   S  +A+  G+ MV ++     +V    V DN+ L     Y   G 
Sbjct: 320 SSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGH 379

Query: 120 FVDQDKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179
              Q ++      I +       P   +  LS    Q   +AK      K++I+DEPT  
Sbjct: 380 IDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRG 439

Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMD 239
           +       ++ +I +L  +G  IV +S +M E+  + D + ++ +G+     P +GL  +
Sbjct: 440 VDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQE 499

Query: 240 KIIAMMVGRS 249
           +++A  +  S
Sbjct: 500 QVLAAAIDTS 509


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: 587
Number of extensions: 32
Number of successful extensions: 9
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: 513
Length adjustment: 34
Effective length of query: 472
Effective length of database: 479
Effective search space:   226088
Effective search space used:   226088
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