GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Azospirillum brasilense Sp245

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__azobra:AZOBR_RS22315
          Length = 497

 Score =  301 bits (770), Expect = 5e-86
 Identities = 181/490 (36%), Positives = 276/490 (56%), Gaps = 13/490 (2%)

Query: 13  ALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFER 72
           AL+  + ++ F  GE+  A+  + F  V+P T   +A+ A G++ D+D A++AA  V  +
Sbjct: 13  ALARELSSKHFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAA--VAAQ 70

Query: 73  GDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYA 132
            +W+     +R  ++ +   +++AH EE+A L  L+TGK +R   R +    + A  ++ 
Sbjct: 71  KEWAKRPVRERGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFG 130

Query: 133 EAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKP 192
               ++ GE    +   L M VREPVGV+ AI+PWN PLLL   K+ PA+ AGN+V++K 
Sbjct: 131 GLAPELKGETIPFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKS 190

Query: 193 SEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQL 252
           +E++PL+ +R+  L     +P GV+N+++G+G E G  L  H D+  + FTGS  TGK +
Sbjct: 191 AEEAPLAVLRVVQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIV 249

Query: 253 LKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGI-FYNQGQVCIAGTRLLLE 311
            K A +  +  V LE GGKS  IV  D  DL QA +   AG+ F  QGQ C A +R+ + 
Sbjct: 250 YKTAAE-KLIPVTLELGGKSPMIVCGDA-DLDQAIAGAIAGMRFTRQGQSCTASSRIFVH 307

Query: 312 ESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG------Q 365
           +SI D F+  LK++    + G PLD +T +GT++     D V S+I  G+  G       
Sbjct: 308 DSIHDAFVEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCS 367

Query: 366 LLLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGL 425
            +           + P IF  V  +  +++EEIFGPV  V R+T  E+ +  AND++YGL
Sbjct: 368 AMPSDPKLTKGLYVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGL 427

Query: 426 GAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHA-LEKFT 484
            A +WTRDL  A     RL+AG V VN        + +GG K SG G++ SL A LE FT
Sbjct: 428 AATIWTRDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFT 487

Query: 485 ELKTIWISLE 494
             KTI I+++
Sbjct: 488 HKKTIIINMK 497


Lambda     K      H
   0.317    0.133    0.389 

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: 557
Number of extensions: 26
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

Related tools

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