Alignments for a candidate for iatA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Sinorhizobium meliloti 1021

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 SMc02325 SMc02325 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Smeli:SMc02325
          Length = 503

 Score =  389 bits (998), Expect = e-112
 Identities = 217/488 (44%), Positives = 310/488 (63%), Gaps = 10/488 (2%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           +SKSFPGVRAL  V L +  G V AL+GENGAGKSTL+KIL+  +  DAGT+   G    
Sbjct: 10  ISKSFPGVRALSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTIRL-GDTET 68

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPR-RLGLVDWSRLRADAQALLND 127
                L   + G+  I+QE  LF ELSVAEN++LG  PR R GL+DW +L ADAQALL  
Sbjct: 69  TFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNADAQALLGR 128

Query: 128 LGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLK 187
            G   +P   +R L +A++ +V IA+A++++AR++IMDEPTAALS +E+  L+ +I  LK
Sbjct: 129 AGADFDPTIRLRDLGIAKKHLVAIARALSVDARVVIMDEPTAALSHKEIHELYDLIERLK 188

Query: 188 ARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEFERRK 247
           A   +V+++SH+  E+  + DRYTV RDG  +  G +ADV   D+VR+MVGR V     K
Sbjct: 189 ADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADVSQDDLVRMMVGRAVGSVYPK 248

Query: 248 RRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFG 307
           +    G  VL V G          P     ++F  R GEI+G  GLVGAGR++  + + G
Sbjct: 249 KEVTIGQPVLTVSG-------YRHPTEFEDINFELRRGEILGFYGLVGAGRSEFMQSLIG 301

Query: 308 ADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALS 367
               +AG V +D + L +RSP +AI+AGI+ VPE+R +QG  +   I +N++LPSL   S
Sbjct: 302 ITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERGRQGAIIGMPIFQNVTLPSLSHTS 361

Query: 368 ALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVD 427
             G ++    E  L   Y  +L ++ A  +  +G LSGGNQQKV++ + +A  PKV+I+D
Sbjct: 362 RSG-FLRLAEEFALAREYTSRLDLRAAALDQDVGTLSGGNQQKVVIAKWLATRPKVIILD 420

Query: 428 EPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQ 487
           EPT+GIDIG+KA VH  +S+LA  G++V+++SSE+ E+M +SDR++V REG +    +  
Sbjct: 421 EPTKGIDIGSKAAVHAFMSELAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERS 480

Query: 488 TATEEGLM 495
             T E L+
Sbjct: 481 ELTAEKLV 488



 Score = 78.6 bits (192), Expect = 5e-19
 Identities = 64/249 (25%), Positives = 113/249 (45%), Gaps = 23/249 (9%)

Query: 257 LKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRV 316
           + +EG++ + P + A   L  VS A   G +  L G  GAG++ L +++ G     AG +
Sbjct: 5   IALEGISKSFPGVRA---LSDVSLALYPGSVTALVGENGAGKSTLVKILTGIYQPDAGTI 61

Query: 317 LVDDKPLRLRSPRDAIQAGI-------MLVPEDRKQQGCFLDHSIRRNLSLPSLKALSAL 369
            + D      +   A +AG+       +L  E    +  FL H+ R    L   K L+A 
Sbjct: 62  RLGDTETTFPTALAASRAGVTAIHQETVLFDELSVAENIFLGHAPRNRFGLIDWKQLNAD 121

Query: 370 GQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEP 429
            Q +  RA  D   T R +              L    +  V + RA+++  +V+I+DEP
Sbjct: 122 AQALLGRAGADFDPTIRLR-------------DLGIAKKHLVAIARALSVDARVVIMDEP 168

Query: 430 TRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTA 489
           T  +      E++ ++  L   G AV+ IS +  E+  ++DR  VFR+G ++ +      
Sbjct: 169 TAALSHKEIHELYDLIERLKADGKAVLFISHKFDEIFRIADRYTVFRDGAMIGEGLIADV 228

Query: 490 TEEGLMAYM 498
           +++ L+  M
Sbjct: 229 SQDDLVRMM 237



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 73/241 (30%), Positives = 104/241 (43%), Gaps = 41/241 (17%)

Query: 29  GEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVL---DPRDA--------PLRRQ 77
           GE+    G  GAG+S  ++ L       AG V   G+VL    P +A        P  R 
Sbjct: 279 GEILGFYGLVGAGRSEFMQSLIGITRPSAGAVKLDGEVLVIRSPAEAIRAGIVYVPEERG 338

Query: 78  QLGIAT---IYQEFNLFPELS---------VAENMYLGREPRRLGLVDWSRLRADAQALL 125
           + G      I+Q   L P LS         +AE   L RE         SRL   A AL 
Sbjct: 339 RQGAIIGMPIFQNVTL-PSLSHTSRSGFLRLAEEFALAREYT-------SRLDLRAAALD 390

Query: 126 NDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAG 185
            D+G           L+   QQ V IAK +    ++II+DEPT  +       +HA ++ 
Sbjct: 391 QDVGT----------LSGGNQQKVVIAKWLATRPKVIILDEPTKGIDIGSKAAVHAFMSE 440

Query: 186 LKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVEFER 245
           L A+ +SVI VS  + E+  M DR  VMR+GR     + +++    +VR   G   + + 
Sbjct: 441 LAAQGLSVIMVSSEIPEIMGMSDRVIVMREGRVAGRYERSELTAEKLVRAAAGIETQADG 500

Query: 246 R 246
           R
Sbjct: 501 R 501


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: 655
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: 515
Length of database: 503
Length adjustment: 34
Effective length of query: 481
Effective length of database: 469
Effective search space:   225589
Effective search space used:   225589
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