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_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_000469325.1:WP_022528026.1
          Length = 515

 Score =  317 bits (813), Expect = 5e-91
 Identities = 185/507 (36%), Positives = 300/507 (59%), Gaps = 26/507 (5%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L +  +SKSF   R LD +D+ V  G V  L+GENGAGKST++K L      D G    
Sbjct: 22  MLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFYL 81

Query: 63  AGQVLD---PRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-RRLGLVDWSRLR 118
            G+ +    P+DA     + GIA ++QE N   + SV +N++LGR P   LG+VD  ++R
Sbjct: 82  DGKEVSFQGPKDA----LENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQMR 137

Query: 119 ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178
            +A  L   LG+ +N   P+R ++V+++QMVEIAKA++ ++++I++DEPT++L  +EVD+
Sbjct: 138 REATELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDK 197

Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVG 238
           L  ++  LK + +S+I++SH++ EV  +CD  +V+RDG  V +   AD  + ++V+ MVG
Sbjct: 198 LFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAMVG 257

Query: 239 RHVEFERRKRRRPP-----GAVVLKVEGV-TPAAPRLSAPGYLRQVSFAARGGEIVGLAG 292
           R ++      R PP     G  +L+V  + T  +P      YL+ ++F+   GEI GL G
Sbjct: 258 RPLD-----NRFPPVDNVVGKTILQVSHLSTKFSP------YLQDITFSVGQGEIFGLYG 306

Query: 293 LVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDH 352
           LVGAGRT+L   IFG    AAGRV  + K     S ++A+  G  ++ E+RK  G FL  
Sbjct: 307 LVGAGRTELLETIFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKG 366

Query: 353 SIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVL 412
           S+  N ++ +L A    G  + E+          Q +  K    +  I  LSGGNQQKV+
Sbjct: 367 SLTFNTTITNLDAYKR-GVALSEQKMTKATLKEIQVMNTKTMGPDELIASLSGGNQQKVI 425

Query: 413 LGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472
           +G+ +   P++ ++DEPTRGID+GAK E+++++  +A  G  ++V+SSE+ E++ +++RI
Sbjct: 426 IGKWLERLPQLFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRI 485

Query: 473 VVFREGVIVADLDAQTATEEGLMAYMA 499
            V   G +   ++ +   +E L+   A
Sbjct: 486 GVMSNGRLAGIVNTKQTNQEELLRLSA 512


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: 544
Number of extensions: 23
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 515
Length of database: 515
Length adjustment: 35
Effective length of query: 480
Effective length of database: 480
Effective search space:   230400
Effective search space used:   230400
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.

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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