GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatA in Azospirillum brasilense Sp245

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 AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__azobra:AZOBR_RS31245
          Length = 518

 Score =  350 bits (898), Expect = e-101
 Identities = 203/509 (39%), Positives = 313/509 (61%), Gaps = 11/509 (2%)

Query: 1   MTLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADA--G 58
           M +L++  ++K+FPGV+ALD V+L V  GE+HAL+GENGAGKSTL+K+LS  +   +  G
Sbjct: 3   MPILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDG 62

Query: 59  TVTFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLR 118
            + F GQ    R      ++LGI  I+QE  L P LS+ EN++LG E    G++DW    
Sbjct: 63  EIRFRGQPQAFRGIA-DSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAAT 121

Query: 119 ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDR 178
             A+ LL  +GL   P+  +  + V +QQ+VEIAKA++   +L+I+DEPTA+L+  + D 
Sbjct: 122 LRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDA 181

Query: 179 LHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD--MVRLM 236
           L  ++   KAR ++ I +SH+L E+  + DR T++RDG  V + D  +  V+   ++R M
Sbjct: 182 LLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGM 241

Query: 237 VGRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGA 296
           VGR +     +R   PG V+ +V+G +   P       +R V+   R GE+VG+AGL+GA
Sbjct: 242 VGRALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGA 301

Query: 297 GRTDLARLIFGAD--PIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSI 354
           GRT+ A  +FG        G+  +D + + + +   A+  G+    EDRK  G  LD+ I
Sbjct: 302 GRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDI 361

Query: 355 RRNLSLPSLKALSALGQWV-DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLL 413
           R N++L +L+ ++   +WV D   E  + E +R++LRI+ AD       LSGGNQQKV+L
Sbjct: 362 RHNVTLANLRGVAK--RWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVL 419

Query: 414 GRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIV 473
            + +   P+VLI+DEPTRGID+GAK E++ +++ L   G  VV+ISSE+ E++ V+DRI 
Sbjct: 420 SKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIY 479

Query: 474 VFREGVIVADLDAQTATEEGLM-AYMATG 501
           V   G +VA++ A  A++E +M A M +G
Sbjct: 480 VMNAGEMVAEMPAAEASQEKIMGAIMRSG 508


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: 699
Number of extensions: 37
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: 518
Length adjustment: 35
Effective length of query: 480
Effective length of database: 483
Effective search space:   231840
Effective search space used:   231840
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 17 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