Alignments for a candidate for fruI in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Azospirillum brasilense Sp245

Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate AZOBR_RS32335 AZOBR_RS32335 PTS fructose transporter subunit IIBC

Query= TCDB::Q1LZ59
         (655 letters)



>FitnessBrowser__azobra:AZOBR_RS32335
          Length = 580

 Score =  328 bits (842), Expect = 3e-94
 Identities = 207/559 (37%), Positives = 297/559 (53%), Gaps = 49/559 (8%)

Query: 105 APDGANDTHLAALAELSQYLLKDGFADKLRQVTNPDDVINLFNATEEEKKEATPA-APVA 163
           A  GA    L    +L +    + FA   R     D V+    A  E+     PA AP  
Sbjct: 53  AAQGAQGVILVGSGDLGE----ERFAGLKRSAAALDAVLRDARAVLEQALATAPAQAPAQ 108

Query: 164 DSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAK 223
                +VA+T+C TGIAHT+MA E +++ A  +G  ++VET G+ G  + LT  +I+ A 
Sbjct: 109 TGTKKIVAITSCPTGIAHTFMAAEGIQQAAQALGHAVRVETQGSVGARDTLTEQEIREAD 168

Query: 224 GVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELINIIL-----DGKAEAYVADNSDLS 278
            V+IAAD  V++ RF GK +        I     L+   L      G A A +AD     
Sbjct: 169 VVLIAADTQVDLARFAGKRVFKSGTKPAINDGRALVERALAEAQPHGTAPA-LADGVAAG 227

Query: 279 SEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNY 338
             A +   A   S  YKHLM+GVS MLPFV+ GG++IA++F +        S    LGN 
Sbjct: 228 KAAKAEHAAAQRSGPYKHLMTGVSFMLPFVVTGGLLIAIAFALGGIYVFEDSQQGTLGN- 286

Query: 339 HEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEF 398
               A+F      AF  M+P  A YIA+SIA++PG+  G V G +A              
Sbjct: 287 ----ALFQIGAKGAFALMVPALAGYIAFSIADRPGITPGMVGGILAAN------------ 330

Query: 399 GEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLV 458
                      + +GFLG +  GF+AG     L + +  + ++LEG+K +L+ PLLG LV
Sbjct: 331 -----------LGAGFLGGIVAGFIAGYATSFLNRNIR-LHKNLEGLKPVLILPLLGSLV 378

Query: 459 TGFLMLFV-NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGT 517
           TG  M++V   P+A     L  +L  + G SA+LLGL++G MMA DMGGP NKAAY F T
Sbjct: 379 TGLAMIYVVGAPVAEALATLSAWLKGMQGSSAILLGLLIGAMMAFDMGGPVNKAAYAFST 438

Query: 518 STLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFI 577
             + +          MA+ MA GMVPPL + +AT LF ++FT+EE +AG    ++G++FI
Sbjct: 439 GLIASQVYTP-----MAAAMAAGMVPPLGLALATKLFADRFTREEREAGNAAGILGIAFI 493

Query: 578 TEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYL 634
           TEGAIPF A DP R IP+ ++G+A+TGA+    G +L  PHGGIFV+ +    ++   Y+
Sbjct: 494 TEGAIPFAARDPLRVIPALVLGAALTGAISMGIGAELKVPHGGIFVLPIPNAVTHLAGYV 553

Query: 635 LYIAVGAVIAGILFGSLRK 653
           + +  G V   +    L++
Sbjct: 554 VALVAGTVTTAVALRFLKR 572



 Score = 40.4 bits (93), Expect = 2e-07
 Identities = 25/72 (34%), Positives = 37/72 (51%)

Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228
           ++AV A         +A EAL+K AA +G  I+VE   + GV N L     + A+GVI+ 
Sbjct: 4   MLAVIAAGDLSTQAVLAAEALRKAAAALGHTIQVEVRSSLGVRNTLPTGAAQGAQGVILV 63

Query: 229 ADKAVEMDRFNG 240
               +  +RF G
Sbjct: 64  GSGDLGEERFAG 75


Lambda     K      H
   0.320    0.137    0.381 

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: 938
Number of extensions: 56
Number of successful extensions: 8
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: 655
Length of database: 580
Length adjustment: 37
Effective length of query: 618
Effective length of database: 543
Effective search space:   335574
Effective search space used:   335574
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 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:

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 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