Alignments for a candidate for mglA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Caulobacter crescentus NA1000

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  360 bits (924), Expect = e-104
 Identities = 189/493 (38%), Positives = 310/493 (62%), Gaps = 6/493 (1%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           LL++S ++KSFPGV+ALD V+L V    +HAL+GENGAGKSTL+K L   +  D+GT+ F
Sbjct: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62

Query: 73  QGKEIDFHSAKEALEN-GISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETK 131
            G+ +D   A    +  GI+ ++QE NL  + SV +NM+LGR P +   VD  ++  + +
Sbjct: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           A+ ++L + ++P A V  L+V++ QM+EIAKA + NA+++IMDEPT++L+ +EV+ L  I
Sbjct: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           I  LK R   ++Y+SH++ E+  +CD  TV+RDG+++A+  +A + +  ++ +MVGR + 
Sbjct: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242

Query: 252 QRFPDKENKPGEVILEVRNLT----SLRQPS-IRDVSFDLHKGEILGIAGLVGAKRTDIV 306
                +   PG V+L+V  +T     L  P  +R VSF    GEI+G+AGLVGA RTD+ 
Sbjct: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302

Query: 307 ETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN 366
             +FG    +AG + +  K +   +  +AI  G  LV E+R+  G +    I  N  + +
Sbjct: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPS 362

Query: 367 IRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426
           ++        +D    +   +     +R+K     T IG LSGGNQQKV++GR +   P+
Sbjct: 363 LKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422

Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
           +L++DEPTRGID+GAK E++Q++++LA  G  +++ISSE+ E++ ++DRI+V   G++  
Sbjct: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482

Query: 487 IVDTKTTTQNEIL 499
            +D +T T+  ++
Sbjct: 483 DLDAQTATEEGLM 495



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 63/259 (24%), Positives = 116/259 (44%), Gaps = 10/259 (3%)

Query: 10  GEYLLEMSGINKSFPGVKA---LDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           G  +L++ G+  + P + A   L  V+   R   I  L G  GAG++ L + +FG     
Sbjct: 253 GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIA 312

Query: 67  SGTILFQGKEIDFHSAKEALENGISMV---HQELNLVLQRSVMDNMWLGRYPTK---GMF 120
           +G +L   K +   S ++A++ GI +V    ++    L  S+  N+ L         G +
Sbjct: 313 AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQW 372

Query: 121 VDQDKMYRETKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSS 179
           VD+       +    +L I + D    +G LS    Q + + +A +   K++I+DEPT  
Sbjct: 373 VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRG 432

Query: 180 LTEKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMD 239
           +       +  ++  L + G  +V IS ++ E+  + D + V R+G  +A       T +
Sbjct: 433 IDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEE 492

Query: 240 KIIAMMVGRSLNQRFPDKE 258
            ++A M   +     PD E
Sbjct: 493 GLMAYMATGTDRVAAPDME 511



 Score = 61.2 bits (147), Expect = 8e-14
 Identities = 47/214 (21%), Positives = 98/214 (45%), Gaps = 8/214 (3%)

Query: 289 GEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINH-GFALVTEER 347
           GE+  + G  GA ++ +++ L       AGT+T  G+ ++  +A       G A + +E 
Sbjct: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPLRRQQLGIATIYQE- 87

Query: 348 RSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSL 407
               ++  L +  N  +        ++GL+D SR+++D Q +++ + +        +  L
Sbjct: 88  --FNLFPELSVAENMYLGR---EPRRLGLVDWSRLRADAQALLNDLGLPL-NPDAPVRGL 141

Query: 408 SGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMP 467
           +   QQ V I + +     ++++DEPT  +       ++ +IA L  +   +I +S  + 
Sbjct: 142 TVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKARSVSVIYVSHRLG 201

Query: 468 ELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501
           E+  + DR  VM +G      D       +++RL
Sbjct: 202 EVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235


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: 565
Number of extensions: 30
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: 515
Length adjustment: 35
Effective length of query: 471
Effective length of database: 480
Effective search space:   226080
Effective search space used:   226080
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, 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

GapMind for catabolism of small carbon sources