Alignments for a candidate for mglA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Phaeobacter inhibens BS107

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  393 bits (1010), Expect = e-114
 Identities = 207/492 (42%), Positives = 318/492 (64%), Gaps = 4/492 (0%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           +L + GI K+FPGV+ALD V+L + P  +HALMGENGAGKSTL+K L GI+Q D G I+ 
Sbjct: 7   VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRETK 131
             + +      +A   GI  +HQEL+L  + SV +N++LG  P K    VD  ++  +T 
Sbjct: 67  AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           AI ++L +  + + RVG LS++  QM+EIA+A + +AK VI DEPT+SLT+ E   LF +
Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           I  L+E+G GI YISH+MEEIF++ D ++VLRDGQ+  T   A    + +  MM+GR L+
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
               +  ++ GEV LEVR L+        DV+F++ +GE++G  GLVGA RT+I ETLFG
Sbjct: 247 LSRNEAHHELGEVALEVRGLSC--GSLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFG 304

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
           +R  ++G+I L G ++   + ++AI  G +LV E+R+  G+   ++   N  +  + + K
Sbjct: 305 LRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLK 364

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
               + D + +    Q+  D + ++TPG +  +G+LSGGNQQK++IG+WL  +P +L++D
Sbjct: 365 AGPFVADGAEIAIFDQY-RDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVD 423

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EPTRGIDVG+K EI+ L+ +LA +G  +I+ISSEMPE+L + DRI+ M +G +     ++
Sbjct: 424 EPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSE 483

Query: 492 TTTQNEILRLAS 503
             T+  ++   S
Sbjct: 484 EVTEENLIAAIS 495



 Score = 95.5 bits (236), Expect = 4e-24
 Identities = 72/248 (29%), Positives = 116/248 (46%), Gaps = 18/248 (7%)

Query: 10  GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69
           GE  LE+ G++         ++VN +VR   +    G  GAG++ + + LFG+    SG+
Sbjct: 257 GEVALEVRGLSCG----SLFEDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGS 312

Query: 70  ILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLGRYPT--KGMFVDQD 124
           I   G E+   S  +A+E GIS+V ++     LVL  +  DNM L +      G FV   
Sbjct: 313 IFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADG 372

Query: 125 KMYRETKAIFDELDIDIDPRAR-----VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179
                  AIFD+    +D R       VG LS    Q I I K  S    ++I+DEPT  
Sbjct: 373 AEI----AIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRG 428

Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMD 239
           +       +  ++R L  +G  ++ IS +M E+  + D +  +  G+ + T     +T +
Sbjct: 429 IDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEE 488

Query: 240 KIIAMMVG 247
            +IA + G
Sbjct: 489 NLIAAISG 496


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: 612
Number of extensions: 32
Number of successful extensions: 7
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: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
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:

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