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 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)



>FitnessBrowser__HerbieS:HSERO_RS05250
          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:

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