GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Tistlia consotensis USBA 355

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_085120648.1 B9O00_RS01470 sugar ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>NCBI__GCF_900177295.1:WP_085120648.1
          Length = 634

 Score =  326 bits (836), Expect = 1e-93
 Identities = 218/515 (42%), Positives = 300/515 (58%), Gaps = 33/515 (6%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L  S + K+F   RAL   DL +  GEVH LLG NGAGKSTL K++S     DAG + +
Sbjct: 14  ILVASGIEKTFDRTRALAGADLELRAGEVHGLLGANGAGKSTLSKVISGHVQRDAGRLVY 73

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122
            G+ L  R       + GIA + QE +L P+LSV EN++L  E  R GL+ +  +R  A 
Sbjct: 74  KGRPLALRSTR-EALEAGIAIVMQETSLAPDLSVLENIFLP-ELGRPGLLSYGSMRRRAV 131

Query: 123 ALLNDLG----LPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178
            LL +LG    LPL  D  V  L+ A++Q+VEIAKA+ L+A LII DEPTA+LS  EV+R
Sbjct: 132 GLLANLGHEHVLPL--DREVARLSAAQRQLVEIAKALALDADLIIFDEPTASLSPSEVER 189

Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGD-VADVEVADMVRLMV 237
           L  I+A L+    ++I+VSHRL EV A+ DR T+MR+G  VA+    A +  A+++R MV
Sbjct: 190 LFDIMAKLRDDGRALIFVSHRLEEVFAITDRVTIMREGATVAASQPTASLTQAEVIRHMV 249

Query: 238 GRHVE-------FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGL 290
           GR +         +    R P    V  VE        L+AP  +R VSF  R GEI+GL
Sbjct: 250 GRDIGALYATPGLQEEDERAP---AVFSVEN-------LAAPPAVRNVSFFVRRGEILGL 299

Query: 291 AGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFL 350
            GLVGAGR++ A  IFG  P +AG + ++ + +  R P DA++AGI  V EDR+ Q    
Sbjct: 300 GGLVGAGRSETAEAIFGLRPRSAGTIRLEGREIAPRKPADAVRAGIGFVAEDRRVQNIVP 359

Query: 351 DHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRI---KMADAETAIGKLSGGN 407
           D S++ NL L  L A    G  +  R  R  VE     L +   ++ DA       SGG 
Sbjct: 360 DLSVKENLLLAHLGAHRGFG--LGYRRRRQKVEELMAALGLPAERLLDANML--NFSGGM 415

Query: 408 QQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMA 467
           QQK+++ R + L PKVLI+DEPT+G+DIG +  ++ +L  +AD GVAVVVISS+  E++ 
Sbjct: 416 QQKIIIARWLLLEPKVLILDEPTKGVDIGTRQAIYGILRRIADEGVAVVVISSDFEELLG 475

Query: 468 VSDRIVVFREGVIVADLDAQTATEEGLMAYMATGT 502
           V +R+VV  +G  +ADL +    EE L    A  T
Sbjct: 476 VCERVVVMSDGNAIADLPSALLDEEKLTLLAAPRT 510


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: 802
Number of extensions: 49
Number of successful extensions: 10
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: 634
Length adjustment: 36
Effective length of query: 479
Effective length of database: 598
Effective search space:   286442
Effective search space used:   286442
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: 53 (25.0 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:

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