Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

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 RR42_RS04800 RR42_RS04800 ABC transporter

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Cup4G11:RR42_RS04800
          Length = 529

 Score =  284 bits (726), Expect = 6e-81
 Identities = 185/508 (36%), Positives = 272/508 (53%), Gaps = 19/508 (3%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           L ++ +SK +PGV A D V LVV  GE+HA+LGENGAGKSTL+KI+  A   DAG + F 
Sbjct: 9   LALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFN 68

Query: 64  GQ---VLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRAD 120
           G    + +P DA    + LGIA ++Q F+LF  L+VAEN+ LG                +
Sbjct: 69  GARAAIHNPHDA----RNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTN 124

Query: 121 AQALLNDL-------GLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSG 173
            + L   +       GLPL P+  V  L+V E+Q VEI +A+    +L+I+DEPT+ L+ 
Sbjct: 125 MKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTP 184

Query: 174 REVDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMV 233
           + V  L   +  L A   S++Y+SH+L E++ +C   TVMR GR     D      A + 
Sbjct: 185 QAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLS 244

Query: 234 RLMVGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSA-PGYLRQVSFAARGGEIVGLAG 292
           RLM+G     E R +  P G   L V  ++   PR  A    L  +S   R GEIVG+AG
Sbjct: 245 RLMIGGEPPREARVQTEP-GVCRLAVRELS--LPRSHAFATELAGISLDLRAGEIVGIAG 301

Query: 293 LVGAGRTDLARLIFGADPIAA-GRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLD 351
           + G G+ +L   + G D  AA   + +D+KP+     R   +AG+  VPE+R  +G    
Sbjct: 302 VSGNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPG 361

Query: 352 HSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKV 411
            S+  N+ L    A       +  +A   L +    +LR+K +        LSGGN QK 
Sbjct: 362 MSLAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKF 421

Query: 412 LLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDR 471
           ++GR +   PKVLIV +PT G+D+GA A++H  L  L   G A++V+S EL E+ A+ DR
Sbjct: 422 IVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDR 481

Query: 472 IVVFREGVIVADLDAQTATEEGLMAYMA 499
           + V  +G +   +  + AT E +  +M+
Sbjct: 482 LHVIAKGRLSPSIPTRDATREQVGLWMS 509



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 62/227 (27%), Positives = 103/227 (45%), Gaps = 6/227 (2%)

Query: 278 VSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIM 337
           VS     GEI  + G  GAG++ L ++IFGA    AG +  +     + +P DA   GI 
Sbjct: 27  VSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAAIHNPHDARNLGIA 86

Query: 338 LVPEDRKQQGCFLDHSIRRNLSLPSLK-ALSALGQWVDERAERDLVETYRQK-LRIKMA- 394
           +V +       F   ++  N++L   + + +A G        + L E  R+  LR  +  
Sbjct: 87  MVFQ---HFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQLAEQIRETALRYGLPL 143

Query: 395 DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVA 454
           +    +  LS G +Q+V + RA+   P++LI+DEPT  +   A   +   L  LA  G +
Sbjct: 144 EPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFITLRQLAAEGTS 203

Query: 455 VVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATG 501
           ++ IS +L E+  +     V R G +    D +  +   L   M  G
Sbjct: 204 ILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMIGG 250


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: 638
Number of extensions: 32
Number of successful extensions: 8
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: 529
Length adjustment: 35
Effective length of query: 480
Effective length of database: 494
Effective search space:   237120
Effective search space used:   237120
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:

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 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