GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Lactobacillus shenzhenensis LY-73

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_022529220.1 L248_RS05900 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000469325.1:WP_022529220.1
          Length = 516

 Score =  265 bits (676), Expect = 4e-75
 Identities = 168/502 (33%), Positives = 265/502 (52%), Gaps = 7/502 (1%)

Query: 4   LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63
           ++V  ++K F    A D + + +  GEVH LLGENGAGK+T++ +LS      +G +   
Sbjct: 8   IEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTSGEILVH 67

Query: 64  GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLG-REPRRLGLVDWSRLRADAQ 122
           GQ +    A     +LGI  ++Q F L    +V EN+ LG  E + LG+++    R    
Sbjct: 68  GQPVHLASAK-DATRLGIGMVHQHFMLVENFTVLENIMLGVEETKGLGVLNRRAARDKVM 126

Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182
           AL    GL ++PDA V  ++V  QQ  EI K +  NA ++I DEPTA L+ +E+  L AI
Sbjct: 127 ALSKQYGLAVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAVLTPQEIKELLAI 186

Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242
              L     +VI +SH+L E++A+    T++R G+ + + D        +  LMVGRHV 
Sbjct: 187 FQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTEKLAELMVGRHVT 246

Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLA 302
           F+R +   P G  +LK+  +     +      +        GGEIVGLAG+ G G+++L 
Sbjct: 247 FQRDRVPMPAGPEILKISHLQVVDNQKVT--RVHDFDLTIHGGEIVGLAGIDGNGQSELV 304

Query: 303 RLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP- 361
           R I G  P A G+V +  +     +PR   ++G+  +PEDR++ G  L  S+  N+SL  
Sbjct: 305 RAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQRYGLILPMSLVDNMSLQV 364

Query: 362 -SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALT 420
            ++   S  G  ++++A     E    +  ++ +      G LSGGNQQK+++ R ++  
Sbjct: 365 YTVAPYSHHGV-LNQKAMVTTTEQLLDQYDVRHSSIMEPAGALSGGNQQKLIIARELSRE 423

Query: 421 PKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVI 480
           P++LI   PTRG+D+GA   +H  L      G A+++IS EL E+  +SDR+ V  +G I
Sbjct: 424 PQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISYELDEIRQLSDRVAVIHQGTI 483

Query: 481 VADLDAQTATEEGLMAYMATGT 502
           V        +E  +   MA  T
Sbjct: 484 VGQAKTSDLSESEIGLLMAGET 505



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 57/235 (24%), Positives = 108/235 (45%), Gaps = 11/235 (4%)

Query: 16  VRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLDPRDA-PL 74
           V  +   DL +  GE+  L G +G G+S L++ ++       G VT AGQ  D   A P 
Sbjct: 274 VTRVHDFDLTIHGGEIVGLAGIDGNGQSELVRAITGLMPTAGGQVTIAGQ--DRTGATPR 331

Query: 75  RRQQLGIATI---YQEFNLFPELSVAENM----YLGREPRRLGLVDWSRLRADAQALLND 127
           +  + G+  I    Q + L   +S+ +NM    Y        G+++   +    + LL+ 
Sbjct: 332 QITRSGVGHIPEDRQRYGLILPMSLVDNMSLQVYTVAPYSHHGVLNQKAMVTTTEQLLDQ 391

Query: 128 LGLPLNPDA-PVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186
             +  +    P   L+   QQ + IA+ ++   +L+I   PT  L    ++ +H+ +   
Sbjct: 392 YDVRHSSIMEPAGALSGGNQQKLIIARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAA 451

Query: 187 KARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241
           +A   +++ +S+ L E++ + DR  V+  G  V     +D+  +++  LM G  V
Sbjct: 452 RAAGHAILLISYELDEIRQLSDRVAVIHQGTIVGQAKTSDLSESEIGLLMAGETV 506


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: 596
Number of extensions: 32
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: 516
Length adjustment: 35
Effective length of query: 480
Effective length of database: 481
Effective search space:   230880
Effective search space used:   230880
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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