Alignments for a candidate for nagF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Azospirillum brasilense Sp245

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate AZOBR_RS32325 AZOBR_RS32325 PTS fructose transporter subunit IIA

Query= TCDB::Q9HXN5
         (842 letters)



>FitnessBrowser__azobra:AZOBR_RS32325
          Length = 846

 Score =  463 bits (1191), Expect = e-134
 Identities = 298/715 (41%), Positives = 402/715 (56%), Gaps = 37/715 (5%)

Query: 139 TNPVEVGAPLLQLSPEKAEQRPANPAPGEGSAQRQVRGRARVAHHGGLHARPAALLRKTA 198
           T+P  + A L + +P  A   PA P          V     V +  GLHARPA    +TA
Sbjct: 141 TDPAALAAALGEDAPVAA---PATPGGDLAERFDWV-----VDYPTGLHARPATAWVETA 192

Query: 199 QGFSSQAELHFAGQVASVDSLVGIMGLGVAEQDEVEVICRGEDSEAALGALLAALASATA 258
           +  +++ ++     VA   +LV ++ LG+   D V V   G+D+ AAL  + A +   TA
Sbjct: 193 RASAARIQVRHGDLVADAKALVALLQLGLRAGDSVVVSAEGDDAVAALARMKATITRLTA 252

Query: 259 GAPKDAP----RAIAPGEPARPAAVAGTLAGVCASPGLASGPLARL--GAISLPAD---- 308
               DA     +A AP     P      + G+ ASPGLA GP+  L   A+S+P +    
Sbjct: 253 REKADAAAAAQKARAPVRGWTPPNPLPAVPGIAASPGLAIGPVHVLPRAAVSVPDEPVPL 312

Query: 309 -DGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGDENEAAIFSAHLALLEDPGLLDAA 367
            +G  R  E      Q L+ + DD        RLG   +EAAIF+A   +L D  L+  A
Sbjct: 313 IEGGDRLHEALSLTRQNLKALADDTA-----RRLG--PSEAAIFAAQAEILNDTDLVTLA 365

Query: 368 DMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERANDLRDLEKRVLR----VLLGDTA 423
             L+ +G G A +WH+A++     L AL N +LA RA DLRD+ +RVL      L    A
Sbjct: 366 CQLMVEGHGVAWSWHQAVERTAAGLAALDNPVLAARAADLRDVGQRVLARIDPALRTGGA 425

Query: 424 PLRVPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATSHVAILARSKGLPCLVALGAG 483
           P       I+ A +++PSD A L  A   GL  A+GG TSH AILAR+ GLP +VA GA 
Sbjct: 426 PDLPDTPCILIAEDLSPSDTAALDMARVIGLATAQGGPTSHTAILARTLGLPAMVAGGAA 485

Query: 484 LLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREEQRRRQQADAQREALTRDGRR 543
           L+EL  G   +LD   GRL LSP A  +      +A+ E ++  ++A     A TRDG  
Sbjct: 486 LMELANGTPAILDGQSGRLHLSPAAADIADARAWIAREEARKAEEEARRGLPARTRDGHE 545

Query: 544 IEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAPDEEEQRNAYQEVLDAMGQRK 603
           +EIGANV  P + A A + GA+ VGL+RTEFLFLER  AP E+EQ   Y+ +L A+  R 
Sbjct: 546 VEIGANVNRPDQVAVALSQGAESVGLMRTEFLFLERGDAPGEDEQYETYRGMLTALEGRP 605

Query: 604 VIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPELLDQQLRALLRVEPLERCR- 662
           +I+R +D+GGDK + +L LP EENP LG+RG  L   RPELL+ QLRAL R       + 
Sbjct: 606 LIVRALDIGGDKQVPHLQLPHEENPFLGVRGARLLLRRPELLETQLRALYRAAKDGGAKD 665

Query: 663 -----ILLPMVSEVDELRAIRRRLGELATQLGIERLPELGVMIEVPSAALLADQLAEHAD 717
                I+ PM++ + E++A+R     +  +L    +P LG+M+EVP+AA+ AD LA H D
Sbjct: 666 GGALSIMFPMITALGEVQALRAACERIRAELDAPAVP-LGIMVEVPAAAIQADVLARHVD 724

Query: 718 FLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQTCAGAARHGRWVGVCGALAS 777
           F SIGTNDL+QYALA+DR H  LA   D+LHPA+LRLI  T  GA RHGRWVGVCG +A 
Sbjct: 725 FFSIGTNDLTQYALAIDRQHPELAAEADSLHPAVLRLIRLTVEGAERHGRWVGVCGGIAG 784

Query: 778 DPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRHAQALLDLGSARAVR 832
           DP    +L GLGV ELS+ P  +  +K R+R  D +  +  AQ  LD  +A AVR
Sbjct: 785 DPFGAALLTGLGVRELSMTPRDIPAVKDRLRGSDLSALKDAAQRALDCETADAVR 839


Lambda     K      H
   0.319    0.136    0.390 

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: 1784
Number of extensions: 103
Number of successful extensions: 6
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: 842
Length of database: 846
Length adjustment: 42
Effective length of query: 800
Effective length of database: 804
Effective search space:   643200
Effective search space used:   643200
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 (21.7 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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