Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E2

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf6N2E2_1008 Inositol transport system ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1008
          Length = 485

 Score =  334 bits (857), Expect = 4e-96
 Identities = 183/471 (38%), Positives = 290/471 (61%), Gaps = 18/471 (3%)

Query: 44  LMGENGAGKSTLLKCLFGIYQKDSG--TILFQGKEIDFHSAK-EALENGISMVHQELNLV 100
           L+GENGAGKST+LK L G    D+G  ++ F G  +  H       E GI  ++QE NL+
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSLEFNGHVLGEHDTPIRRQEVGIITIYQEFNLI 60

Query: 101 LQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEI 160
              SV +NM+LGR P +  FVD  +M+ + + + D+L + I PR  V  LSV++ QM+EI
Sbjct: 61  ADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITPRTMVRKLSVAEQQMVEI 120

Query: 161 AKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVT 220
           AKA + NAK++IMDEPT++L+ +EV+ L  II  LK +G  I+Y+SHK+ E+   CD  T
Sbjct: 121 AKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEVKACCDRYT 180

Query: 221 VLRDGQWIATEPLAGLTMDKIIAMMVGRSLNQRFPDKENKPGEVILEVRNLT-------- 272
           + RDG +I +  +  +++D I+ +MVGR +          PGEV+L+V++++        
Sbjct: 181 IFRDGAYITSGDVCDVSVDDIVRLMVGRDVEFVRKPLTGAPGEVMLKVQSVSRTAAGGGR 240

Query: 273 SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNA 332
           SL    + D+S D+  GEI+G AGLVGA RT++   +FG      G I ++G+Q++   +
Sbjct: 241 SLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVIFGADGCDEGMIYVNGRQVSPFKS 300

Query: 333 -NEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVID 391
             E I  G ALV E+R+    +    I +N  + ++   +     +D+   +++TQ + D
Sbjct: 301 PREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLGGLQRWGMFIDD---RAETQLIQD 357

Query: 392 ---SMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQL 448
               +R+K       IG+LSGGNQQKVI+ R +  +P++L++DEPTRGIDVGAK E++QL
Sbjct: 358 YQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKPKVLIVDEPTRGIDVGAKAEVHQL 417

Query: 449 IAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEIL 499
           + ++A+ G  +I+ISSE+PE++ ++DRI+    G ++GIV     T+  ++
Sbjct: 418 LFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQITGIVSADEATEELLM 468



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 61/238 (25%), Positives = 113/238 (47%), Gaps = 20/238 (8%)

Query: 6   TPSSGEYLLEMSGINKSFPG------VKALDNVNLKVRPHSIHALMGENGAGKSTLLKCL 59
           T + GE +L++  ++++  G         L ++++ VR   I    G  GAG++ L + +
Sbjct: 218 TGAPGEVMLKVQSVSRTAAGGGRSLHATPLLDMSVDVRAGEIVGFAGLVGAGRTELARVI 277

Query: 60  FGIYQKDSGTILFQGKEID-FHSAKEALENGISMVHQELN---LVLQRSVMDNM---WLG 112
           FG    D G I   G+++  F S +E +  G+++V ++       L  S+  NM    LG
Sbjct: 278 FGADGCDEGMIYVNGRQVSPFKSPREGIAAGVALVPEDRKQQACFLSHSIRWNMSLPSLG 337

Query: 113 RYPTKGMFVDQDKMYRETKAIFD---ELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNA 168
                GMF+D      ET+ I D    L I + +    +GTLS    Q + +A+  +   
Sbjct: 338 GLQRWGMFIDD---RAETQLIQDYQKRLRIKMSNDSVAIGTLSGGNQQKVILARCMALKP 394

Query: 169 KIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQ 226
           K++I+DEPT  +       +  ++  +   G  ++ IS ++ E+  + D +   R+GQ
Sbjct: 395 KVLIVDEPTRGIDVGAKAEVHQLLFDMARAGVAVIVISSELPEVMAVSDRIVTFREGQ 452



 Score = 62.0 bits (149), Expect = 5e-14
 Identities = 57/212 (26%), Positives = 101/212 (47%), Gaps = 12/212 (5%)

Query: 294 IAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIY 353
           + G  GA ++ I++ L G +   AG  +L   + N H   E   H   +  +E     IY
Sbjct: 1   LLGENGAGKSTILKILAGAQPADAGQGSL---EFNGHVLGE---HDTPIRRQEVGIITIY 54

Query: 354 AYLD-IGFNSLISNIRNYKNKV--GLLDNSRMKSDTQWVIDSMRVK-TPGHRTQIGSLSG 409
              + I   S+  N+   +  +  G +D  +M SD Q V+D + +  TP  RT +  LS 
Sbjct: 55  QEFNLIADMSVAENMYLGREPLRHGFVDWKQMFSDAQHVLDDLGLHITP--RTMVRKLSV 112

Query: 410 GNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPEL 469
             QQ V I + L    +++++DEPT  +      +++++I +L  KG  II +S ++ E+
Sbjct: 113 AEQQMVEIAKALTMNAKLIIMDEPTAALSGREVDKLHEIITDLKAKGISIIYVSHKLNEV 172

Query: 470 LGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
               DR  +  +G      D    + ++I+RL
Sbjct: 173 KACCDRYTIFRDGAYITSGDVCDVSVDDIVRL 204


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: 561
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 506
Length of database: 485
Length adjustment: 34
Effective length of query: 472
Effective length of database: 451
Effective search space:   212872
Effective search space used:   212872
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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