Alignments for a candidate for iatA in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Collimonas pratensis Ter91

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 WP_082793282.1 CPter91_RS01720 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_001584185.1:WP_082793282.1
          Length = 518

 Score =  385 bits (989), Expect = e-111
 Identities = 207/494 (41%), Positives = 316/494 (63%), Gaps = 7/494 (1%)

Query: 2   TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVT 61
           ++L +S V+K FPGV ALD+V   +  GEVHA+ GENGAGKSTL+KI+S  + AD G + 
Sbjct: 21  SILSLSNVTKRFPGVLALDRVSFDLKKGEVHAICGENGAGKSTLMKIISGVYRADQGAII 80

Query: 62  FAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADA 121
           + G      ++    Q  GIA I+QE NL P LSVAEN++L REP++   VD  ++ A+A
Sbjct: 81  YKGSECR-FESSTEAQIAGIAIIHQELNLVPHLSVAENIFLAREPKKGLFVDRKKMNANA 139

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
           Q  L+ L + + P   V+ L++A+QQMVEIAKA++LNA ++IMDEPT++L+  E  +L  
Sbjct: 140 QICLDRLKVNIKPADLVKSLSIAQQQMVEIAKALSLNAEVLIMDEPTSSLTETETGQLFN 199

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           II  LK   V ++Y+SHRL E++ + DR TVMRDG+FV++ + +++ +  +V  MVGR +
Sbjct: 200 IINDLKRNGVGIVYISHRLDELRHIVDRVTVMRDGKFVSTDNFSEITIDKIVSKMVGRAL 259

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
           E    +R+  P       E        LS       + FA R GEI+G AGL+GAGRT++
Sbjct: 260 EDAFPERKSTP------TEKTLLTVRNLSRQDDFGPIDFALRQGEILGFAGLIGAGRTEV 313

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           AR IFGADP+++G++ + +  L++  P DAI+ GI  + EDRK  G  ++ S+  N++L 
Sbjct: 314 ARAIFGADPVSSGQIYLGETELKITCPVDAIKHGIAYLSEDRKSHGLAINMSLASNITLT 373

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
           ++ A++    ++    E    +TY   L IK    +  +  LSGGNQQK+++ + +    
Sbjct: 374 NMPAVTDRFGFIKFGQEETAAQTYIDALGIKTPSTQKIVKNLSGGNQQKIVIAKWLFRGS 433

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481
           ++L  DEPTRGID+GAK  ++Q+L +LA  G+ VV+ISSEL E++ ++DR+ VF EG I 
Sbjct: 434 RILFFDEPTRGIDVGAKFAIYQLLDELAAKGIGVVMISSELPEILGMTDRVAVFHEGKIA 493

Query: 482 ADLDAQTATEEGLM 495
             L+ +  ++E +M
Sbjct: 494 VILNTRETSQEEIM 507



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 65/244 (26%), Positives = 118/244 (48%), Gaps = 12/244 (4%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           +L +  VT   P + A   L +VSF  + GE+  + G  GAG++ L ++I G      G 
Sbjct: 22  ILSLSNVTKRFPGVLA---LDRVSFDLKKGEVHAICGENGAGKSTLMKIISGVYRADQGA 78

Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH-SIRRNLSLPSLKALSALGQWVD 374
           ++      R  S  +A  AGI ++ ++       + H S+  N+ L         G +VD
Sbjct: 79  IIYKGSECRFESSTEAQIAGIAIIHQELN----LVPHLSVAENIFLAREPKK---GLFVD 131

Query: 375 ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGID 434
            +      +    +L++ +  A+  +  LS   QQ V + +A++L  +VLI+DEPT  + 
Sbjct: 132 RKKMNANAQICLDRLKVNIKPADL-VKSLSIAQQQMVEIAKALSLNAEVLIMDEPTSSLT 190

Query: 435 IGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGL 494
                ++  +++DL   GV +V IS  L E+  + DR+ V R+G  V+  +    T + +
Sbjct: 191 ETETGQLFNIINDLKRNGVGIVYISHRLDELRHIVDRVTVMRDGKFVSTDNFSEITIDKI 250

Query: 495 MAYM 498
           ++ M
Sbjct: 251 VSKM 254



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 56/246 (22%), Positives = 110/246 (44%), Gaps = 12/246 (4%)

Query: 2   TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVT 61
           TLL V  +S+          +D  +  GE+    G  GAG++ + + +  A    +G + 
Sbjct: 274 TLLTVRNLSRQDD----FGPIDFALRQGEILGFAGLIGAGRTEVARAIFGADPVSSGQI- 328

Query: 62  FAGQVLDPRDAPLRRQQLGIATIYQE---FNLFPELSVAENMYLGREPR---RLGLVDWS 115
           + G+       P+   + GIA + ++     L   +S+A N+ L   P    R G + + 
Sbjct: 329 YLGETELKITCPVDAIKHGIAYLSEDRKSHGLAINMSLASNITLTNMPAVTDRFGFIKFG 388

Query: 116 RLRADAQALLNDLGLPL-NPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGR 174
           +    AQ  ++ LG+   +    V+ L+   QQ + IAK +   +R++  DEPT  +   
Sbjct: 389 QEETAAQTYIDALGIKTPSTQKIVKNLSGGNQQKIVIAKWLFRGSRILFFDEPTRGIDVG 448

Query: 175 EVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVR 234
               ++ ++  L A+ + V+ +S  L E+  M DR  V  +G+     +  +    +++ 
Sbjct: 449 AKFAIYQLLDELAAKGIGVVMISSELPEILGMTDRVAVFHEGKIAVILNTRETSQEEIMH 508

Query: 235 LMVGRH 240
              GR+
Sbjct: 509 HASGRN 514


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: 587
Number of extensions: 29
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 515
Length of database: 518
Length adjustment: 35
Effective length of query: 480
Effective length of database: 483
Effective search space:   231840
Effective search space used:   231840
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 24 2021. 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