GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Pseudomonas litoralis 2SM5

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_090274723.1 BLU11_RS14925 NADP-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q5P171
         (474 letters)



>NCBI__GCF_900105005.1:WP_090274723.1
          Length = 486

 Score =  286 bits (732), Expect = 1e-81
 Identities = 170/462 (36%), Positives = 249/462 (53%), Gaps = 13/462 (2%)

Query: 16  GSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLMHALGAALE 75
           G   ++VNPA+GE    V    A    +A+AAA+AA P W R    ER  ++      + 
Sbjct: 25  GQRVEIVNPASGERLGSVPDMGADETRRAIAAAQAAQPVWRRRTAKERAGVLRRWYELIL 84

Query: 76  AHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPV--EVIQDND-DAR 132
            H  +L  ++T E GKPL    G     E+  A ++    A+    V  +VI  +  D R
Sbjct: 85  QHQEDLARIMTAEQGKPLTEARG-----EIAYAASFIEWFAEEAKRVYGDVIPGHQTDKR 139

Query: 133 IEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVELAN-A 191
           + V ++P+GV  +ITPWN+P  +      PAL AG  +V+KP+  TP + +  V LA  A
Sbjct: 140 LIVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLKPAPQTPFSALALVALAEQA 199

Query: 192 ILPPGVLNIVTG----ESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLEL 247
            LP G+L++VT        VG  +  +P + K+ FTGST  G  +MQ  A +LK+L+LEL
Sbjct: 200 GLPAGLLSVVTAGVDNARAVGGELCANPVVRKLSFTGSTAVGIQLMQQCAPSLKKLSLEL 259

Query: 248 GGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKET 307
           GGN   IV  D D       +    + N GQTC C  R+YV D++Y+    +LA   +  
Sbjct: 260 GGNAPFIVFEDADLDEAVEGVMISKYRNAGQTCVCANRIYVQDAVYDAFAEKLAAAVRRL 319

Query: 308 VVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADA 367
            VGDG+ EG   GP+ N   +  +Q  ++DA   GA +L+GGK  + GG FFEPT++   
Sbjct: 320 EVGDGMREGVTTGPLINAEAVSKIQRHLQDALDGGATLLAGGKPHALGGLFFEPTILTGV 379

Query: 368 KDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECG 427
              M +  EE FGPV P+ R+ D  +V+ +AN+ E GL    +++D ++   +A  LE G
Sbjct: 380 DSSMLIAREETFGPVAPLFRFDDEADVVRQANDTEFGLAAYFYARDLSRVFRVAEALEYG 439

Query: 428 TAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTL 469
              +N        APFGG+K SGLG E  +YG++EY  I+ L
Sbjct: 440 MVGINTGLISTEVAPFGGMKASGLGREGSKYGMDEYLEIKYL 481


Lambda     K      H
   0.317    0.136    0.405 

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: 31
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: 474
Length of database: 486
Length adjustment: 34
Effective length of query: 440
Effective length of database: 452
Effective search space:   198880
Effective search space used:   198880
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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