GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Paucidesulfovibrio gracilis DSM 16080

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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  216 bits (549), Expect = 2e-60
 Identities = 156/503 (31%), Positives = 257/503 (51%), Gaps = 29/503 (5%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           L+ +  ++K F  V A D + L +  G V ALLGENGAGKSTL+ +L+  +  DAGT+  
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 63  AGQVL---DPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119
            G+ +     RDA     + GI  +YQ F L   ++VAEN+ LG+E      ++   +R 
Sbjct: 84  DGKPVRFSSARDAI----EAGIGMVYQHFMLVESMTVAENVLLGQEGSFF--LNPKEMRN 137

Query: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179
             Q L    GL ++P A V  L++ E+Q VEI K +  ++R++I DEPTA L+ RE   L
Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197

Query: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEV---ADMVRLM 236
              +  +  +  S++++SH+L EV A+ D   ++R GR    G+ ++ EV   AD+   M
Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRI--EGEFSESEVTSKADLACRM 255

Query: 237 VGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGA 296
           VG+ V  E  +   P G  VL+V  +T           L  ++F    GE+V + G+ G 
Sbjct: 256 VGKEVLLEVDREAMPHGDAVLQVRNLTGIG--------LEDITFDLHQGEVVAVVGVAGN 307

Query: 297 GRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356
           G+  L   I G        + +  K  R    + + +  +  +PEDR       + ++  
Sbjct: 308 GQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVD 367

Query: 357 NLSLPSLKALSALGQWVD-ERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415
           NL L + +   A G W+D ++A RD  E  + K  I+         +LSGGN QK +L R
Sbjct: 368 NLLLTTRQGF-ARGPWLDKKKAARDTTELIK-KFDIRPGRIAALAWQLSGGNLQKSVLAR 425

Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475
            +   P++++ ++PT+G+DI A  +V   L    ++   +++++ +L E + ++DR+ V 
Sbjct: 426 ELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREM-AGILLVTGDLNEALQLADRVAVI 484

Query: 476 REG---VIVADLDAQTATEEGLM 495
             G    + +  D Q     GLM
Sbjct: 485 YRGRFMDVFSVSDKQKVNRIGLM 507



 Score = 89.4 bits (220), Expect = 3e-22
 Identities = 71/274 (25%), Positives = 131/274 (47%), Gaps = 15/274 (5%)

Query: 242 EFERRKRRRPP-GAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTD 300
           + +R KR  PP G  ++ ++G+T    ++ A      +S     G +  L G  GAG++ 
Sbjct: 9   QLDRSKRDVPPQGIPLVSIKGLTKRFGKVVAND---DISLNIYPGRVKALLGENGAGKST 65

Query: 301 LARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSL 360
           L  ++ G     AG + +D KP+R  S RDAI+AGI +V         +    +  ++++
Sbjct: 66  LMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIGMV---------YQHFMLVESMTV 116

Query: 361 PSLKALSALGQW-VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
                L   G + ++ +  R+ V+    +  + + D    +  LS G +Q+V + + +  
Sbjct: 117 AENVLLGQEGSFFLNPKEMRNRVQELSVRYGLDI-DPAARVSDLSMGEKQRVEILKLLYR 175

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
             +VLI DEPT  +       + + L  +A+ G ++V IS +L EV+AV+D I + R+G 
Sbjct: 176 DSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGR 235

Query: 480 IVADLDAQTATEEGLMAYMATGTDRVAAPDMERL 513
           I  +      T +  +A    G + +   D E +
Sbjct: 236 IEGEFSESEVTSKADLACRMVGKEVLLEVDREAM 269



 Score = 41.2 bits (95), Expect = 9e-08
 Identities = 53/232 (22%), Positives = 97/232 (41%), Gaps = 22/232 (9%)

Query: 19  LDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRD------- 71
           L+ +   +  GEV A++G  G G+  L++ +         T+   G+    RD       
Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRW--RDFYAKPSW 343

Query: 72  ----APLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLND 127
               A +   +LG+AT  +  NL   L +       R P     +D  +   D   L+  
Sbjct: 344 KNSLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKK 398

Query: 128 LGL-PLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186
             + P    A    L+    Q   +A+ +    RLI+ ++PT  L     +++   +  L
Sbjct: 399 FDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL--L 456

Query: 187 KARSVS-VIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237
            AR ++ ++ V+  L E   + DR  V+  GRF+    V+D +  + + LM+
Sbjct: 457 AAREMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508


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: 578
Number of extensions: 33
Number of successful extensions: 8
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: 514
Length adjustment: 35
Effective length of query: 480
Effective length of database: 479
Effective search space:   229920
Effective search space used:   229920
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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:

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:

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:

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