GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Azospirillum brasilense Sp245

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase

Query= BRENDA::P80668
         (499 letters)



>FitnessBrowser__azobra:AZOBR_RS19635
          Length = 485

 Score =  313 bits (803), Expect = 7e-90
 Identities = 182/476 (38%), Positives = 276/476 (57%), Gaps = 9/476 (1%)

Query: 23  YIDGRPGPAQSEKRLAIFDPATGQEIASTADANEADVDNAVMSAWRAFVSRRWAGRLPAE 82
           Y++G    A S K  A+ +PATG+E+A  AD    +   A+ +A  A  +  W  +   E
Sbjct: 14  YVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPA--WRAKTAKE 71

Query: 83  RERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGLTTKIAGKT 142
           R  IL R+ +L+    E+LA L TLEQGK +A +R  EV    +++ + A    ++ G  
Sbjct: 72  RAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARG-EVAYGASFIEWFAEEGKRVYGDV 130

Query: 143 LDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSIVIKPSETT 202
               IP   G + +    KEP+GVVA I PWNFP  +   KV PALAAGC+IV+KP+E T
Sbjct: 131 ----IPSFAGNK-RIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDT 185

Query: 203 PLTMLRVAELASEAGIPDGVFNVVTGSGAVC-GAALTSHPHVAKISFTGSTATGKGIART 261
           PL+ L +AELA  AG+P GVFN+VTGS  V  G  LT+ P V K+SFTGST  GK + R 
Sbjct: 186 PLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMRQ 245

Query: 262 AADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYIEAPLFDT 321
           +AD + +V+LELGG  P IV  DAD    ++G +   + N GQ C  ++R+ ++A ++D 
Sbjct: 246 SADTVKKVSLELGGNAPFIVFDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDA 305

Query: 322 LVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELIRGSNGPAGE 381
             +   +AVK ++VG GM       P+++    +KV   + DA A+ A++  G       
Sbjct: 306 FAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGLG 365

Query: 382 GYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTASVWTQNLS 441
           G +  PT++     ++R+ REE+FGPV  L +     +A+++ANDTE+GL A  +++++ 
Sbjct: 366 GTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDIG 425

Query: 442 QALEYSDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDGWCETKSVCV 497
           +    +++L+ G V +N   L     PFGG+KQSG GR+     ++ + E K +CV
Sbjct: 426 RVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCV 481


Lambda     K      H
   0.318    0.133    0.402 

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: 597
Number of extensions: 32
Number of successful extensions: 4
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: 499
Length of database: 485
Length adjustment: 34
Effective length of query: 465
Effective length of database: 451
Effective search space:   209715
Effective search space used:   209715
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.

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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