GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1243 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243
          Length = 521

 Score =  254 bits (650), Expect = 4e-72
 Identities = 159/474 (33%), Positives = 251/474 (52%), Gaps = 12/474 (2%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L + ++SK +PG  A D +DL +  GE+HALLGENGAGKSTL+KI+     AD+G + + 
Sbjct: 14  LQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQ 73

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWS--RLRADA 121
           GQ +  R+ P + + LGI  ++Q F+LF  LSVA+N+ L      +G    +  +L    
Sbjct: 74  GQRVTMRN-PAQARGLGIGMVFQHFSLFETLSVAQNIALA-----MGAAAGTPKQLEPKI 127

Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181
           + +    G+ L P+  V  L++ E+Q VEI + +  + RL+I+DEPT+ L+ +E D L  
Sbjct: 128 REVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 187

Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
            +  L A   S++++SH+LGEV+A+C   TV+R GR       A      + +LMVG   
Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMVGEAA 247

Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
           E      +       L V G++   P       L+ + F  R GEIVG+AG+ G G+ +L
Sbjct: 248 ELITDYPKVMGADAFLSVTGLSWHNPDPFGCS-LKNIDFDVRSGEIVGVAGVAGNGQDEL 306

Query: 302 ARLIFGADPIA---AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358
             L+ G + +    +  +    +P+    P    + G+  VP +R   G   + S+  N 
Sbjct: 307 LALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADNA 366

Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418
            L + +        V     + L E   ++  +K  D+      LSGGN QK +LGR + 
Sbjct: 367 LLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGREIL 426

Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472
             PK+L+   PT G+D+GA A +H+ L  L D G A++VIS +L E+  + DR+
Sbjct: 427 QQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRL 480



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 59/233 (25%), Positives = 107/233 (45%), Gaps = 13/233 (5%)

Query: 18  ALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAA---DAGTVTFAGQVLDPRDAPL 74
           +L  +D  V  GE+  + G  G G+  L+ +LS        D+ T++F GQ +     P 
Sbjct: 279 SLKNIDFDVRSGEIVGVAGVAGNGQDELLALLSGEERLPRDDSATISFGGQPV-AHLRPD 337

Query: 75  RRQQLGIATIYQE---FNLFPELSVAENMYLGREPRRL---GLVDWSRLRADAQALLNDL 128
            R++LG+A +  E       PELS+A+N  L    + L   GLV   +++A A+ ++   
Sbjct: 338 ARRKLGLAFVPAERLGHGAVPELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRF 397

Query: 129 GLPLNPD--APVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186
           G+   PD  AP R L+    Q   + + +    +L++   PT  +       +H  +  L
Sbjct: 398 GVK-TPDSLAPARSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIAL 456

Query: 187 KARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239
           +    +++ +S  L E+  +CDR   +  G+        D  ++D+   M G+
Sbjct: 457 RDAGAAILVISEDLDELFQICDRLGALCGGQLSPLQATVDTHLSDVGGWMAGQ 509



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 58/209 (27%), Positives = 97/209 (46%), Gaps = 12/209 (5%)

Query: 272 PGYLRQ--VSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPR 329
           PG L    +  +   GEI  L G  GAG++ L ++I+G     +G ++   + + +R+P 
Sbjct: 24  PGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQGQRVTMRNPA 83

Query: 330 DAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKL 389
            A   GI +V +       F   S+ +N++L    A     Q   E   R++ + Y   L
Sbjct: 84  QARGLGIGMVFQ---HFSLFETLSVAQNIALAMGAAAGTPKQL--EPKIREVSQRYGMAL 138

Query: 390 RIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLA 449
                + E  +  LS G +Q+V + R +    ++LI+DEPT  +      E+   L  LA
Sbjct: 139 -----EPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLA 193

Query: 450 DLGVAVVVISSELAEVMAVSDRIVVFREG 478
             G +++ IS +L EV A+     V R G
Sbjct: 194 AEGCSILFISHKLGEVRALCHSATVLRGG 222


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: 602
Number of extensions: 29
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: 521
Length adjustment: 35
Effective length of query: 480
Effective length of database: 486
Effective search space:   233280
Effective search space used:   233280
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.

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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