GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Acidovorax sp. GW101-3H11

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= metacyc::MONOMER-15732
         (497 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1496
          Length = 500

 Score =  513 bits (1320), Expect = e-150
 Identities = 257/487 (52%), Positives = 338/487 (69%), Gaps = 2/487 (0%)

Query: 8   LPATRAFLERKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQ 67
           L   +   ER++   IG     A SGR L   +PAT  V+ E P +DA D+ RAV +A++
Sbjct: 11  LQGAKFLSERRVGNVIGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAADIARAVASAQR 70

Query: 68  AFDDSPWSRLRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFL 127
           AFD   W  LRP +R+ LL+RL++L+ER A +L+ LE L +GK   +A+ +DVQ   +F+
Sbjct: 71  AFDSHVWRGLRPADREKLLFRLSELIERHADELSALETLQSGKLQGIARAIDVQAGAEFV 130

Query: 128 RYMAGWATKIEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPAL 187
           RYMAGWATK+EG T++ S+P+ P  Q+  + RRE +GVVGAIV WNFPL +A WK+ PAL
Sbjct: 131 RYMAGWATKLEGQTLDNSIPI-PGPQWVTYTRREPVGVVGAIVPWNFPLAIALWKIAPAL 189

Query: 188 ATGCTIVLKPADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTF 247
           A GCT+VLKP+++TPL+ L+LA L  EAG P GV NVV G G  AGAAL  HPGV KL+F
Sbjct: 190 AAGCTVVLKPSEDTPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIAHPGVRKLSF 249

Query: 248 TGSTEVGKLIGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCA 307
           TGST VGK++G AA++NM R TLELGGKSP +VM DA+  + A G AT IFF+QGQVC A
Sbjct: 250 TGSTAVGKVVGHAAVENMARFTLELGGKSPAVVMEDADPSQVAQGIATGIFFHQGQVCTA 309

Query: 308 GSRLYVHRKHFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELG 367
            SRL VHR  +  V+ ++AGIA GM++G+G D A Q GPL S     RV  +I   +  G
Sbjct: 310 SSRLLVHRSLYRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARVMDFIASAKAEG 369

Query: 368 ATVACGGEG-FGPGYFVKPTVIVDVDQRHRLVQEEIFGPVLVAMPFDDLDEVIGMANDNP 426
           AT+  GGE     G FV+PT+  D   + R+V+EE+FGPVL   PFDD+++ I  AND P
Sbjct: 370 ATLVAGGERVHDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDVEDAIAAANDTP 429

Query: 427 YGLGASIWSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEH 486
           YGL AS+W+  L+  HR++PR+++G VWVN H+ LD  LP GG K SG GR++G AA+E 
Sbjct: 430 YGLAASLWTQSLSHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGTGRDLGRAAVEG 489

Query: 487 YTELKSV 493
           +TELKSV
Sbjct: 490 FTELKSV 496


Lambda     K      H
   0.320    0.137    0.413 

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: 656
Number of extensions: 29
Number of successful extensions: 3
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: 497
Length of database: 500
Length adjustment: 34
Effective length of query: 463
Effective length of database: 466
Effective search space:   215758
Effective search space used:   215758
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: 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