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_085124750.1 B9O00_RS21270 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_900177295.1:WP_085124750.1
          Length = 500

 Score =  379 bits (973), Expect = e-109
 Identities = 222/499 (44%), Positives = 313/499 (62%), Gaps = 18/499 (3%)

Query: 9   VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68
           +SK+F GV ALD+VD  +  GEVHALLGENGAGKSTLIKI++ A AADAG +   G+ + 
Sbjct: 14  ISKAFAGVPALDRVDFTLHPGEVHALLGENGAGKSTLIKIMTGALAADAGEMRLDGRAVA 73

Query: 69  PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLNDL 128
                  R  LGI+T+YQE NL P LSVA N+ LGREPRR GL+ W   R  A+A L  L
Sbjct: 74  VGSTAEARA-LGISTVYQEVNLVPTLSVARNVTLGREPRRFGLISWRAAREKARARLKRL 132

Query: 129 GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGLKA 188
            L ++ +  +    VA QQ+V IA+A+  ++R++++DEPTA+L  +E   L  I+  LKA
Sbjct: 133 SLEIDVERALGSFPVAVQQLVAIARALEEDSRVLVLDEPTASLDAQETRLLFRILRDLKA 192

Query: 189 RSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE-FERRK 247
           + ++V+++SH L +V  + DR +V+R+GR V S   A +   +++ LM+GR +E  E+R 
Sbjct: 193 QGMAVVFISHFLDQVYEISDRISVLRNGRLVGSAATAALPQRELITLMLGRELERVEQRA 252

Query: 248 RRRP--PGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLI 305
              P   GA VL       AA +L    ++       R GE +GLAGL+G+GRT+ A+LI
Sbjct: 253 AAAPKAAGAPVL-------AAEKLGRRRWIEPFDLVLRAGEAIGLAGLLGSGRTETAKLI 305

Query: 306 FGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKA 365
           FGA    +GR+ +D  PL   SPR A++ GI   PEDRK +G  LD S+R N+    L A
Sbjct: 306 FGAVRADSGRLTLDGAPLGHASPRRALRRGIAFCPEDRKAEGLVLDLSVRENI----LLA 361

Query: 366 LSALGQW---VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPK 422
           L     W   +    +R L E   + L I  +DAE  +G+LSGGNQQKV+L RA+A  P+
Sbjct: 362 LQTKRGWLRPLPRDEQRRLAEAMIEALGIATSDAEKPVGQLSGGNQQKVVLARALASKPR 421

Query: 423 VLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVA 482
           VL++DEPTRGID+GA AE+  ++  L   G+A++V SSEL E++AVSDR+ V R+  IV 
Sbjct: 422 VLVLDEPTRGIDVGAHAEIVALVRRLCAEGLALLVASSELDEIVAVSDRVAVLRDRRIVG 481

Query: 483 DLDAQTATEEGLMAYMATG 501
           ++     T E ++  +A G
Sbjct: 482 EIAGAEITRETIIELIAGG 500


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: 659
Number of extensions: 39
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 500
Length adjustment: 34
Effective length of query: 481
Effective length of database: 466
Effective search space:   224146
Effective search space used:   224146
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.

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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:

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