Alignments for a candidate for mglA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Herbaspirillum seropedicae SmR1

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  439 bits (1129), Expect = e-127
 Identities = 228/506 (45%), Positives = 338/506 (66%), Gaps = 8/506 (1%)

Query: 2   GSTISPPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFG 61
           G   S  S   ++ +R + K FPGV ALDN    +    +HALMGENGAGKSTL+K L G
Sbjct: 11  GVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSG 70

Query: 62  IYQKDSGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GM 119
           +YQ+DSG I+  GK V+    ++A   GI ++HQELNL+   S   N+++GR P K  G+
Sbjct: 71  VYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGL 130

Query: 120 FVDQDKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179
           F+D+D++ +   AIF  + +D+DP   VG L+V++ QM+EIAKA S++++++IMDEPT++
Sbjct: 131 FIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAA 190

Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMD 239
           L   E+  LF IIR L+ +G GIVYISHKM+E+ Q+ D ++++RDG++IAT P++   MD
Sbjct: 191 LNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMD 250

Query: 240 KIIAMMVGRSLN--QRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGL 297
            II+MMVGR+L+  QR P   ++  DV+LEVR L   R  +IRDVSF L KGEILG AGL
Sbjct: 251 TIISMMVGRALDGEQRIPPDTSR-NDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGL 307

Query: 298 VGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLD 357
           +GA RT++   +FG     +G I +HG K    +  +A+ HG   ++E+R+  G+   +D
Sbjct: 308 MGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367

Query: 358 IGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVII 417
           +  N  +S++  +  +VG +D   ++   Q  +  + +KTP    Q   LSGGNQQK++I
Sbjct: 368 VQANIALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVI 426

Query: 418 GRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRIL 477
            +WLL   +IL  DEPTRGIDVGAK EIY+L+  LA++GK I++ISSE+PE+L ++ R+L
Sbjct: 427 AKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVL 486

Query: 478 VMSNGLVSGIVDTKTTTQNEILRLAS 503
           VM  G ++G +     TQ +I++LA+
Sbjct: 487 VMCEGRITGELARADATQEKIMQLAT 512



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 60/247 (24%), Positives = 119/247 (48%), Gaps = 16/247 (6%)

Query: 11  EYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSI 70
           + +LE+RG+N+     +A+ +V+  +R   I    G  GAG++ + + +FG    ++G I
Sbjct: 275 DVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEI 330

Query: 71  VFQGKEVDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGMFVDQD 124
           +  G +    S  +A+ +GI  + ++     L +   V  N+ L   GR+   G F+DQ 
Sbjct: 331 IIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FMDQR 389

Query: 125 KMYQDTKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
            + +  +    +L I    ++ +AR+  LS    Q I IAK    +  I+  DEPT  + 
Sbjct: 390 AIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGID 447

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241
               + ++ ++  L E+G  IV IS ++ E+ ++   + ++ +G+            +KI
Sbjct: 448 VGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKI 507

Query: 242 IAMMVGR 248
           + +   R
Sbjct: 508 MQLATQR 514


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: 624
Number of extensions: 27
Number of successful extensions: 8
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: 520
Length adjustment: 35
Effective length of query: 471
Effective length of database: 485
Effective search space:   228435
Effective search space used:   228435
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