Alignments for a candidate for iatA in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Cereibacter sphaeroides ATCC 17029

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_011842128.1 RSPH17029_RS15870 autoinducer 2 ABC transporter ATP-binding protein LsrA

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000015985.1:WP_011842128.1
          Length = 491

 Score =  324 bits (831), Expect = 4e-93
 Identities = 195/491 (39%), Positives = 298/491 (60%), Gaps = 19/491 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           L ++  VSKS+  VR L  V   V  GE+HALLG NGAGKSTL+KIL+   A   G V  
Sbjct: 5   LAELRSVSKSYAAVRVLKGVHFSVRAGEIHALLGGNGAGKSTLMKILAGLVAPSGGEVRL 64

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            G  L P   P + Q +G+  + QE ++FP  +V +N+ +G  P+  G       RA  +
Sbjct: 65  GGAPLVPA-TPAQAQAMGLYLVPQEAHIFPNQTVLQNIAVGM-PKPAGAY-----RARVE 117

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
           AL+  LG+ L+PDA    L +A++Q+VEI + +   A+++I+DEPT+AL+  EV  L   
Sbjct: 118 ALIAQLGVSLSPDAKAATLEIADRQIVEILRGLLREAKVLILDEPTSALTPHEVRTLFGH 177

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242
           +  L+A    ++++SH+L E++A+ DR TV+RDG  V +  +     A+++  M      
Sbjct: 178 MRALRAEGHGLVFISHKLHELRAVADRITVLRDGHVVFAEAMETSPDAEILAAMSPGVTA 237

Query: 243 FERRKRRRP-PGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301
            + R+R R   GA VL ++       RLS  G++ ++S + R GEI+GL G+VGAGRT+L
Sbjct: 238 LDARERMREIAGAPVLTLD-------RLSGEGFV-EISLSLRPGEILGLTGVVGAGRTEL 289

Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361
           A  + G    + GRV +     R R P +A+QAG++ + EDR+Q G FL+  +  N+S  
Sbjct: 290 AETLVGLRAPSGGRVTLGGHDFRARGPAEAMQAGLVHLSEDRQQYGLFLEAPLYWNVS-- 347

Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421
           SL     L  ++    ER   E YR +L I+  +A+  +G+LSGGNQQKVLL + +A  P
Sbjct: 348 SL-VHGTLPFFLRPGRERRRFEQYRAQLGIRCEEADQPVGRLSGGNQQKVLLAKCLAAAP 406

Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481
           KVLI+DEPTRG+D+GA+ ++++++ DLA+ G AV++ISS+  EV  ++DRI V   G + 
Sbjct: 407 KVLILDEPTRGVDVGARNDIYRIIEDLAEQGTAVLLISSDFDEVRRLADRIAVMAGGHLA 466

Query: 482 ADLDAQTATEE 492
            +L A  +T+E
Sbjct: 467 GELPAGASTDE 477



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 69/239 (28%), Positives = 118/239 (49%), Gaps = 15/239 (6%)

Query: 275 LRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQA 334
           L+ V F+ R GEI  L G  GAG++ L +++ G    + G V +   PL   +P  A   
Sbjct: 21  LKGVHFSVRAGEIHALLGGNGAGKSTLMKILAGLVAPSGGEVRLGGAPLVPATPAQAQAM 80

Query: 335 GIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMA 394
           G+ LVP++      F + ++ +N+         A+G      A R  VE    +L + ++
Sbjct: 81  GLYLVPQEAH---IFPNQTVLQNI---------AVGMPKPAGAYRARVEALIAQLGVSLS 128

Query: 395 -DAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGV 453
            DA+ A  +++  ++Q V + R +    KVLI+DEPT  +       +   +  L   G 
Sbjct: 129 PDAKAATLEIA--DRQIVEILRGLLREAKVLILDEPTSALTPHEVRTLFGHMRALRAEGH 186

Query: 454 AVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLMAYMATGTDRVAAPDMER 512
            +V IS +L E+ AV+DRI V R+G +V     +T+ +  ++A M+ G   + A +  R
Sbjct: 187 GLVFISHKLHELRAVADRITVLRDGHVVFAEAMETSPDAEILAAMSPGVTALDARERMR 245


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: 636
Number of extensions: 38
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: 491
Length adjustment: 34
Effective length of query: 481
Effective length of database: 457
Effective search space:   219817
Effective search space used:   219817
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 10 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:

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