Alignments for a candidate for treF in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Azospirillum brasilense Sp245

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate AZOBR_RS22875 AZOBR_RS22875 glucoamylase

Query= CAZy::ABK72415.1
         (668 letters)



>FitnessBrowser__azobra:AZOBR_RS22875
          Length = 598

 Score =  379 bits (974), Expect = e-109
 Identities = 243/620 (39%), Positives = 331/620 (53%), Gaps = 37/620 (5%)

Query: 42  IADYGFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILDRGA-GHFRLGPYGVSVPAA 100
           I DY  L DCET  L+S+ GS++WLC PR DS + F A+L     G + L P        
Sbjct: 5   IEDYALLGDCETAALLSAEGSIDWLCWPRFDSDACFAALLGTPENGRWLLRPSDPDARTT 64

Query: 101 RRYLPGSLILETTWQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVR 160
           RRY   SLILET ++T  G + + D +                  P   +A  I+ R + 
Sbjct: 65  RRYRGDSLILETEFETAEGAVTMIDFM------------------PPRGEASDIV-RILH 105

Query: 161 CVSGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNLRIGIE 220
              G V + M     F Y  V       GP    AIA     PD    + L T+  I  E
Sbjct: 106 GRRGRVAMRMDLTLRFGYGHVVPWVTRIGPHTLRAIA----GPDM---VVLHTSAPIHGE 158

Query: 221 GREARARTRLTEGDNV-FVALSWSKH-PAPQTYEEAADKMWKTSEAWRQWINVGDFPDHP 278
                A   + EG+++ FV +    H P P+  + A   + +T   W +W     +    
Sbjct: 159 NLSTVADFTVAEGESISFVMIYSPSHLPLPEPVD-AERALAETERFWAEWSGRCTYSGL- 216

Query: 279 WRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALWGLYT 338
           WR  + RS +TLK LTY PTG ++AAPTTSLPE   G RNWDYRY W+RD+T  L  L  
Sbjct: 217 WRDAVLRSLVTLKALTYRPTGGIVAAPTTSLPEQLGGVRNWDYRYCWLRDATLTLLALMN 276

Query: 339 LGLDREADDFFSF-IADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRPVRI 397
            G  +EA D+  + +  ++G+       +Q+MYG+ GER L+E E+  L GY+ + PVR+
Sbjct: 277 AGYLQEARDWRDWGLRTIAGSPQ----QIQIMYGIAGERRLLEWEVPWLPGYEGASPVRV 332

Query: 398 GNGAYNQRQHDIWGTMLDSVYLHAKSREQIPDALWPVLKNQVEEAIKHWKEPDRGIWEVR 457
           GN A  Q Q D++G M+D+ +       +I    W V    ++     W +PD GIWEVR
Sbjct: 333 GNAAAPQLQLDVYGEMMDAAHQARMRGIEIRPEGWQVQCALLDHMESVWDQPDEGIWEVR 392

Query: 458 GEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLARGVDK-RGVLT 516
           G  +HFT SK+M WVA+DR  K AE  G  +   +W+A+ + I  DV A+G  K R    
Sbjct: 393 GGAKHFTHSKVMAWVAVDRMVKSAEKFGLDAPLDRWKALRQAIFDDVCAKGYSKERNSFV 452

Query: 517 QRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETDDGLAGE 576
           Q YG   +DA+LL+  +  FLP DDPRI+ TV AI  EL +DGLV+RYR E TDDGL   
Sbjct: 453 QHYGASHVDAALLMLPMLGFLPVDDPRIQGTVAAIERELLQDGLVMRYRTERTDDGLPDG 512

Query: 577 EGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLGNFPQAF 636
           EG F  CSFWL    V  G  + A+ L  RLL+  + L L +EE +    R +GNFPQAF
Sbjct: 513 EGVFLACSFWLADVYVLQGRQAEAEALFNRLLALRNDLGLLSEEYDTTAKRLVGNFPQAF 572

Query: 637 THLALINAVVHVIRAEEEAD 656
           +H+ALIN   ++ RAE+ A+
Sbjct: 573 SHIALINTAFNLTRAEKPAE 592


Lambda     K      H
   0.319    0.135    0.426 

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: 1217
Number of extensions: 62
Number of successful extensions: 5
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: 668
Length of database: 598
Length adjustment: 38
Effective length of query: 630
Effective length of database: 560
Effective search space:   352800
Effective search space used:   352800
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: 54 (25.4 bits)

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

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Protein sequences (fasta format)
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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