GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Tistlia consotensis USBA 355

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_085126169.1 B9O00_RS28465 multiple monosaccharide ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_900177295.1:WP_085126169.1
          Length = 509

 Score =  350 bits (897), Expect = e-101
 Identities = 205/500 (41%), Positives = 307/500 (61%), Gaps = 8/500 (1%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAAD--AGTV 60
           +L++  ++K+FPGV ALD V+L V  GE+HAL GENGAGKSTL+KILS  +      G +
Sbjct: 4   ILEMRDITKTFPGVVALDNVNLQVRQGEIHALAGENGAGKSTLMKILSGVYPYGDYQGDI 63

Query: 61  TFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120
            + G+V   R       + GI  I+QE  L PELS+AEN++LG E  R G++DW      
Sbjct: 64  VYEGEVKKFRGIADSEAE-GIVIIHQELALVPELSIAENIFLGNEIARFGVIDWHATNEL 122

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           A   L  +GL  +P   V+ L + +QQ+VEIAKA++   +L+I+DEPT++L+ ++   L 
Sbjct: 123 AADHLKWVGLKESPRTKVQDLGLGKQQLVEIAKALSKEVKLLILDEPTSSLNEQDSAALL 182

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVA--DMVRLMVG 238
            ++A  + R +S I +SH+L E+  + D  TV+RDG  V++ D A   ++  D++R MVG
Sbjct: 183 KLLAEFRERGISSILISHKLNEISQVADSITVLRDGTTVSTLDCAAASISEDDIIRDMVG 242

Query: 239 RHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGR 298
           R +      R    G ++L+VE  +   P+      ++  SF  R GE+VGLAGL+GAGR
Sbjct: 243 RSLSDRFPPRHPKIGELLLEVEHWSVRHPQHLDRRVVKDASFTVRRGEVVGLAGLMGAGR 302

Query: 299 TDLARLIFGADPIA--AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRR 356
           T+LA  +FG    A  AG V +  K + + +   AI AG+    EDRK  G  LD  ++ 
Sbjct: 303 TELAMSLFGRSYGADIAGEVRIRGKAVDVSTVERAIAAGLCYATEDRKSYGLVLDDIVKH 362

Query: 357 NLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRA 416
           NL+L +L+ + A G  +D   E  + E YR++L IK +        LSGGNQQKV+LG+ 
Sbjct: 363 NLTLANLEGV-ANGPVIDHAREIRVAEDYRRRLNIKTSSIAQKTLNLSGGNQQKVVLGKW 421

Query: 417 MALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFR 476
           +   P+VLI+DEPTRGID+GAK E++ +++DLA  G  ++VISSE+ E++ + DRI V  
Sbjct: 422 LFADPEVLILDEPTRGIDVGAKYEIYSIITDLAAAGKGILVISSEMPELLGICDRIYVMN 481

Query: 477 EGVIVADLDAQTATEEGLMA 496
            G +V +L A  A++E +M+
Sbjct: 482 AGRLVGELPAAEASQEKIMS 501



 Score = 53.9 bits (128), Expect = 1e-11
 Identities = 56/229 (24%), Positives = 100/229 (43%), Gaps = 9/229 (3%)

Query: 17  RALDQVDLVVGVGEVHALLGENGAGKSTL-IKILSAAHAAD-AGTVTFAGQVLDPRDAPL 74
           R +      V  GEV  L G  GAG++ L + +   ++ AD AG V   G+ +D      
Sbjct: 277 RVVKDASFTVRRGEVVGLAGLMGAGRTELAMSLFGRSYGADIAGEVRIRGKAVDVSTVE- 335

Query: 75  RRQQLGIATIYQE---FNLFPELSVAENMYLGR-EPRRLG-LVDWSRLRADAQALLNDLG 129
           R    G+    ++   + L  +  V  N+ L   E    G ++D +R    A+     L 
Sbjct: 336 RAIAAGLCYATEDRKSYGLVLDDIVKHNLTLANLEGVANGPVIDHAREIRVAEDYRRRLN 395

Query: 130 LPLNPDAP-VRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
           +  +  A     L+   QQ V + K +  +  ++I+DEPT  +       +++II  L A
Sbjct: 396 IKTSSIAQKTLNLSGGNQQKVVLGKWLFADPEVLILDEPTRGIDVGAKYEIYSIITDLAA 455

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237
               ++ +S  + E+  +CDR  VM  GR V     A+     ++ +++
Sbjct: 456 AGKGILVISSEMPELLGICDRIYVMNAGRLVGELPAAEASQEKIMSMII 504


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: 680
Number of extensions: 34
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 509
Length adjustment: 35
Effective length of query: 480
Effective length of database: 474
Effective search space:   227520
Effective search space used:   227520
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