Alignments for a candidate for iatA in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Pseudarthrobacter sulfonivorans Ar51

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_058930145.1 AU252_RS07280 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_001484605.1:WP_058930145.1
          Length = 506

 Score =  354 bits (909), Expect = e-102
 Identities = 204/505 (40%), Positives = 311/505 (61%), Gaps = 15/505 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           LL+V  ++K F GV+AL  VDL V  GEVH ++G+NGAGKSTLIK LS  H  D G + +
Sbjct: 10  LLEVRGLTKRFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPDGGEIRW 69

Query: 63  AG-QVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADA 121
            G Q+  PR  P     LGIAT+YQE ++   LSVAEN++LG E    G++   +  A A
Sbjct: 70  EGKQITLPR--PTAALDLGIATMYQELDVVDGLSVAENIFLGHERSTGGVLHVKKTNAIA 127

Query: 122 QALLNDLGL-PLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           + LL  LG   L+P   V  L+ A +Q+V +A+A++ + +LIIMDEP+A L   EV  L 
Sbjct: 128 RTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDSGEVSNLF 187

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASG-DVADVEVADMVRLMVGR 239
            ++  L A+ ++V+Y+SHRL E++ + DR +V++DGR  A+G  V D + ++++RLM GR
Sbjct: 188 RVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSELIRLMTGR 247

Query: 240 HVE--FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297
            V   F  RK       VVL V+        L   G+  +VS   R GEI+G AGLVG+ 
Sbjct: 248 DVANVFPERKPVPADAPVVLDVDN-------LELYGHFEKVSLTVRAGEILGFAGLVGSK 300

Query: 298 RTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRN 357
           R+++   I+GA   ++GRV V+ K LR  S   A+ AGI L PE+RK QG  LD  + +N
Sbjct: 301 RSEILETIYGARKASSGRVSVNGKALRPGSVTSAVNAGIGLSPEERKSQGLILDEPLFKN 360

Query: 358 LSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAM 417
           ++L + +  + +G +++E AER+        L ++ AD +     LSGGNQQK+LL R +
Sbjct: 361 VTLSTFERFARMG-YLNEAAERNAAREQIAALELRPADPDRPARTLSGGNQQKILLARWL 419

Query: 418 ALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFRE 477
                VL++DEPTRG+D+GA++E++ ++  LA+ G A++V+SSE+ EV+ ++D ++V  +
Sbjct: 420 VHGTSVLLLDEPTRGVDVGARSEIYDLIRKLAEAGTAIIVVSSEIEEVLGLADNVLVIDD 479

Query: 478 GVIVADLDAQTATEEGLMAYMATGT 502
           G ++    A    E G++  +  G+
Sbjct: 480 GKVLTQTKASDIDEHGVLDLVMKGS 504



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 64/248 (25%), Positives = 118/248 (47%), Gaps = 9/248 (3%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           +L+V G+T    R +    L+ V      GE+  + G  GAG++ L + + G      G 
Sbjct: 10  LLEVRGLTK---RFAGVQALKGVDLQVLPGEVHCVMGQNGAGKSTLIKTLSGVHQPDGGE 66

Query: 316 VLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDE 375
           +  + K + L  P  A+  GI  + ++          S+  N+ L   ++   +   +  
Sbjct: 67  IRWEGKQITLPRPTAALDLGIATMYQELDVVDGL---SVAENIFLGHERSTGGV---LHV 120

Query: 376 RAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDI 435
           +    +  T  ++L        T +G LS  N+Q V + RA++   K++I+DEP+  +D 
Sbjct: 121 KKTNAIARTLLKRLGHGSLSPSTEVGTLSAANKQIVSMARALSRDTKLIIMDEPSAILDS 180

Query: 436 GAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEGLM 495
           G  + + +V+ +L   G+AVV IS  L E+  + DRI V ++G   A+  + T T++  +
Sbjct: 181 GEVSNLFRVVRELTAQGIAVVYISHRLEEIRQIGDRISVIKDGRSTANGLSVTDTQKSEL 240

Query: 496 AYMATGTD 503
             + TG D
Sbjct: 241 IRLMTGRD 248


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: 630
Number of extensions: 46
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: 506
Length adjustment: 35
Effective length of query: 480
Effective length of database: 471
Effective search space:   226080
Effective search space used:   226080
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:

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 2024 update 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