Alignments for a candidate for mglA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudarthrobacter sulfonivorans Ar51

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate WP_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  337 bits (864), Expect = 6e-97
 Identities = 189/490 (38%), Positives = 304/490 (62%), Gaps = 11/490 (2%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72
           LLE+RG+ K F GV+AL  V+L V P  +H +MG+NGAGKSTL+K L G++Q D G I +
Sbjct: 10  LLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPDGGEIRW 69

Query: 73  QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYQDTKA 132
           +GK++       AL+ GI+ ++QEL++V   SV +N++LG   + G  +   K     + 
Sbjct: 70  EGKQITLPRPTAALDLGIATMYQELDVVDGLSVAENIFLGHERSTGGVLHVKKTNAIART 129

Query: 133 IFDELDI-DIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           +   L    + P   VGTLS +  Q++ +A+A S + K++IMDEP++ L   EV++LF +
Sbjct: 130 LLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDSGEVSNLFRV 189

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDK--IIAMMVGRS 249
           +R+L  +G  +VYISH++EEI Q+ D I++++DG+  A   L   D  K  +I +M GR 
Sbjct: 190 VRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANG-LSVTDTQKSELIRLMTGRD 248

Query: 250 LNQRFPDKENKPGD--VILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVE 307
           +   FP+++  P D  V+L+V +L          VS  +  GEILG AGLVG+KR++I+E
Sbjct: 249 VANVFPERKPVPADAPVVLDVDNLELYGH--FEKVSLTVRAGEILGFAGLVGSKRSEILE 306

Query: 308 TLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNI 367
           T++G R+ SSG ++++GK +   +   A+N G  L  EER+S G+     +  N  +S  
Sbjct: 307 TIYGARKASSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDEPLFKNVTLSTF 366

Query: 368 RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEI 427
             +  ++G L+ +  ++  +  I ++ ++         +LSGGNQQK+++ RWL+    +
Sbjct: 367 ERFA-RMGYLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQKILLARWLVHGTSV 425

Query: 428 LMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGI 487
           L+LDEPTRG+DVGA+ EIY LI +LA+ G  II++SSE+ E+LG+ D +LV+ +G V  +
Sbjct: 426 LLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLADNVLVIDDGKV--L 483

Query: 488 VDTKTTTQNE 497
             TK +  +E
Sbjct: 484 TQTKASDIDE 493



 Score = 82.8 bits (203), Expect = 3e-20
 Identities = 63/251 (25%), Positives = 127/251 (50%), Gaps = 12/251 (4%)

Query: 254 FPDKENKPGDVILEVRHLTS--LRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
           F + + +P   +LEVR LT       +++ V   +  GE+  + G  GA ++ +++TL G
Sbjct: 2   FEEDQPRP---LLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSG 58

Query: 312 IREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
           + +   G I   GK+I       A++ G A + +E     +   L +  N  + + R+  
Sbjct: 59  VHQPDGGEIRWEGKQITLPRPTAALDLGIATMYQE---LDVVDGLSVAENIFLGHERSTG 115

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
              G+L   +  +  + ++  +   +    T++G+LS  N+Q V + R L    +++++D
Sbjct: 116 ---GVLHVKKTNAIARTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMD 172

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EP+  +D G    +++++ EL  +G  ++ IS  + E+  I DRI V+ +G  +    + 
Sbjct: 173 EPSAILDSGEVSNLFRVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSV 232

Query: 492 TTTQ-NEILRL 501
           T TQ +E++RL
Sbjct: 233 TDTQKSELIRL 243



 Score = 76.6 bits (187), Expect = 2e-18
 Identities = 53/224 (23%), Positives = 106/224 (47%), Gaps = 8/224 (3%)

Query: 30  DNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVFQGKEVDFHSAKEALENG 89
           + V+L VR   I    G  G+ +S +L+ ++G  +  SG +   GK +   S   A+  G
Sbjct: 279 EKVSLTVRAGEILGFAGLVGSKRSEILETIYGARKASSGRVSVNGKALRPGSVTSAVNAG 338

Query: 90  ISMVHQELN---LVLQRSVMDNMWLG---RYPTKGMFVDQDKMYQDTKAIFDELDI-DID 142
           I +  +E     L+L   +  N+ L    R+   G ++++       +     L++   D
Sbjct: 339 IGLSPEERKSQGLILDEPLFKNVTLSTFERFARMG-YLNEAAERNAAREQIAALELRPAD 397

Query: 143 PRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGI 202
           P     TLS    Q I +A+   +   ++++DEPT  +     + ++ +IRKL E G  I
Sbjct: 398 PDRPARTLSGGNQQKILLARWLVHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAI 457

Query: 203 VYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMV 246
           + +S ++EE+  L D + ++ DG+ +       +D   ++ +++
Sbjct: 458 IVVSSEIEEVLGLADNVLVIDDGKVLTQTKASDIDEHGVLDLVM 501


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: 613
Number of extensions: 37
Number of successful extensions: 9
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: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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 Apr 09 2024. 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 2024 update 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