GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Herbaspirillum seropedicae SmR1

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05250 HSERO_RS05250 D-ribose
           transporter ATP binding protein
          Length = 520

 Score =  439 bits (1128), Expect = e-127
 Identities = 228/504 (45%), Positives = 340/504 (67%), Gaps = 8/504 (1%)

Query: 4   STTPSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIY 63
           + + SS   ++ +  + K FPGV ALDN   ++    +HALMGENGAGKSTL+K L G+Y
Sbjct: 13  AASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72

Query: 64  QKDSGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK--GMFV 121
           Q+DSG IL  GK ++    ++A   GI ++HQELNL+   S   N+++GR P K  G+F+
Sbjct: 73  QRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132

Query: 122 DQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           D+D++ R+  AIF  + +D+DP   VG L+V++ QM+EIAKA S++++++IMDEPT++L 
Sbjct: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241
             E+  LF IIR L+ +G GIVYISHKM+E+ Q+ D V+V+RDG++IAT P+   +MD I
Sbjct: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252

Query: 242 IAMMVGRSLN--QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVG 299
           I+MMVGR+L+  QR P   ++  +V+LEVR L   R  +IRDVSF L KGEILG AGL+G
Sbjct: 253 ISMMVGRALDGEQRIPPDTSR-NDVVLEVRGLN--RGRAIRDVSFTLRKGEILGFAGLMG 309

Query: 300 AKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIG 359
           A RT++   +FG     AG I +HG +    +  +A+ HG   ++E+R+  G+   +D+ 
Sbjct: 310 AGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQ 369

Query: 360 FNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGR 419
            N  +S++  +  +VG +D   ++   Q  +  + +KTP    Q   LSGGNQQK++I +
Sbjct: 370 ANIALSSMGRF-TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428

Query: 420 WLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVM 479
           WLL   +IL  DEPTRGIDVGAK EIY+L+  LA++GK I++ISSE+PE+L ++ R+LVM
Sbjct: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488

Query: 480 SNGLVSGIVDTKTTTQNEILRLAS 503
             G ++G +     TQ +I++LA+
Sbjct: 489 CEGRITGELARADATQEKIMQLAT 512



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 64/250 (25%), Positives = 120/250 (48%), Gaps = 16/250 (6%)

Query: 8   SSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           S  + +LE+ G+N+     +A+ +V+  +R   I    G  GAG++ + + +FG    ++
Sbjct: 272 SRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA 327

Query: 68  GTILFQGKEIDFHSAKEALENGISMVHQE---LNLVLQRSVMDNMWL---GRYPTKGMFV 121
           G I+  G +    S  +A+ +GI  + ++     L +   V  N+ L   GR+   G F+
Sbjct: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FM 386

Query: 122 DQDKMYRETKAIFDELDI---DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTS 178
           DQ  +    +    +L I    ++ +AR+  LS    Q I IAK    +  I+  DEPT 
Sbjct: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTR 444

Query: 179 SLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTM 238
            +     + ++ ++  L E+G  IV IS ++ E+ ++   V V+ +G+       A  T 
Sbjct: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504

Query: 239 DKIIAMMVGR 248
           +KI+ +   R
Sbjct: 505 EKIMQLATQR 514


Lambda     K      H
   0.318    0.136    0.384 

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: 607
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 ( 7.3 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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