Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  279 bits (714), Expect = 2e-79
 Identities = 191/497 (38%), Positives = 267/497 (53%), Gaps = 32/497 (6%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L ++ ++K F  + A D + L +  GEV ALLGENGAGKSTL+ IL   + ADAGTV  
Sbjct: 5   ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            GQ L P   P      GI  ++Q F L   LSV +N+ LG +P     +D    R    
Sbjct: 65  DGQPLPPGQ-PRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVL 123

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
           AL    GL + P A V  L+V E+Q VEI KA+   AR++I+DEPTA L+  E + L + 
Sbjct: 124 ALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFST 183

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242
           +A L A  +SVI++SH+L EV  + DR  V+R G+ VA    A    A++  LMVGR V 
Sbjct: 184 LAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVA 243

Query: 243 FERRKRRR-----------PPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLA 291
              R  RR           PP   VL +E V   A   +    LR+VS   R GEIVG+A
Sbjct: 244 MPERVARRSAEDGANGNAAPP---VLALEHV--GARAANGRALLREVSLQVRAGEIVGIA 298

Query: 292 GLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLD 351
           G+ G G+  LA L  G    + GR+ +  KP+  + PR  I AG+  VPEDR   G   D
Sbjct: 299 GVSGNGQAALAELASGMLEASEGRITLAGKPMSAK-PRAWIGAGVARVPEDRHAIGVVGD 357

Query: 352 -----HSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGG 406
                +++   LS P       + +   +R  RDLV     +  ++ A  +     +SGG
Sbjct: 358 LAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLV----ARFDVRTAGIDVPARTMSGG 413

Query: 407 NQQKVLLGRAMAL-----TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSE 461
           N QK++LGRA+++      P++++  +PT G+DIGA A V   L D A  G AV++IS +
Sbjct: 414 NMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISED 473

Query: 462 LAEVMAVSDRIVVFREG 478
           L E+ A++DRI V   G
Sbjct: 474 LDELHALADRIAVMHAG 490



 Score = 94.0 bits (232), Expect = 1e-23
 Identities = 79/245 (32%), Positives = 123/245 (50%), Gaps = 14/245 (5%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           +L++ G+T     L A      +S   + GE++ L G  GAG++ L  ++FG     AG 
Sbjct: 5   ILRLAGITKRFGPLVAND---DISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGT 61

Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQW-V 373
           V VD +PL    PR A+ AGI +V     Q     D+ S+  N+ L +      L QW +
Sbjct: 62  VEVDGQPLPPGQPRAALTAGIGMV----HQHFTLADNLSVLDNIMLGT----QPLWQWRL 113

Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433
           D  A R  V    ++  + +   +  +G+LS G +Q+V + +A+    +VLI+DEPT  +
Sbjct: 114 DGHAARGKVLALAERFGLAVRP-QARVGELSVGERQRVEIVKALYRGARVLILDEPTAVL 172

Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493
                  +   L+ L   G++V+ IS +L EV+ VSDRI V R G +VA   A   T+  
Sbjct: 173 TPHEAETLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAE 232

Query: 494 LMAYM 498
           L   M
Sbjct: 233 LAELM 237



 Score = 60.8 bits (146), Expect = 1e-13
 Identities = 60/241 (24%), Positives = 105/241 (43%), Gaps = 23/241 (9%)

Query: 15  GVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDAPL 74
           G   L +V L V  GE+  + G +G G++ L ++ S    A  G +T AG+ +  +  P 
Sbjct: 278 GRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMSAK--PR 335

Query: 75  RRQQLGIATIYQE---FNLFPELSVAENMYLGR--EPR--RLGLVDWSRLRADAQALLND 127
                G+A + ++     +  +L+V EN    +  EPR  R G++     RA AQ    D
Sbjct: 336 AWIGAGVARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIR----RAAAQRFARD 391

Query: 128 LGLPLNP-----DAPVRGLTVAEQQMVEIAKAMTLNA-----RLIIMDEPTAALSGREVD 177
           L    +      D P R ++    Q + + +A+++       RL++  +PT  L    V 
Sbjct: 392 LVARFDVRTAGIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVA 451

Query: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237
            + A +        +V+ +S  L E+ A+ DR  VM  G    +   A   + ++   M 
Sbjct: 452 YVRARLLDAAREGAAVLLISEDLDELHALADRIAVMHAGHLTEARPTAAWTLGELGLAMA 511

Query: 238 G 238
           G
Sbjct: 512 G 512


Lambda     K      H
   0.320    0.136    0.380 

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: 670
Number of extensions: 35
Number of successful extensions: 10
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: 515
Length of database: 530
Length adjustment: 35
Effective length of query: 480
Effective length of database: 495
Effective search space:   237600
Effective search space used:   237600
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 (21.8 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