GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Paenisporosarcina indica PN2

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_075617845.1 GY23_RS03715 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>NCBI__GCF_001939075.1:WP_075617845.1
          Length = 502

 Score =  400 bits (1029), Expect = e-116
 Identities = 206/477 (43%), Positives = 300/477 (62%), Gaps = 5/477 (1%)

Query: 22  LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81
           LYI+G+F  +A G T    NP T E +  + E QA D++KAV AAR+AFD+G W+TM  A
Sbjct: 20  LYINGEFTSAAGGTTMKNMNPFTNELINEVAEGQAEDINKAVAAAREAFDKGPWKTMKLA 79

Query: 82  SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWC-TKITG 140
            R   +Y++ADL++E    +A LE +D G PI++T    +  A E+ R+YA    +++ G
Sbjct: 80  KRMAYIYRIADLIDEEVERIAYLEAMDTGLPISQTKKM-VGRASENFRFYARMVESRLVG 138

Query: 141 QTIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSA 200
               V   + NYT + PVGV G I PWN P ++  WK+  ALATG T+VLKPAE +PLSA
Sbjct: 139 DAYQVDDEFINYTINTPVGVAGLITPWNAPFMLETWKVAPALATGNTVVLKPAELSPLSA 198

Query: 201 LYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSI 260
             LAE+I +A  P GV N++ G GE AG+AL  H  V  I+FTG T+ G  I+  +A ++
Sbjct: 199 NLLAEIIHRADLPKGVFNVVHGVGETAGDALVKHPDVQLISFTGETKTGSTIIKNSADTL 258

Query: 261 KRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEM 320
           K  ++ELGGKSP I+  DA+ ++A+   + G+    G+ C A SR+F+ +   D+ ++ +
Sbjct: 259 KSCSMELGGKSPIIVFDDADFERALDACVWGIYSFNGERCTANSRLFLQETIKDQFIEAL 318

Query: 321 ASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFE--AGYF 378
               E ++ G  L   T++GPL+ K   ++V SY+   K+EGA+ +T  + P E   G F
Sbjct: 319 KERVEKIKIGDPLEAVTEVGPLIDKGHFQKVKSYLDIAKEEGAEVIT-ANIPDELTKGNF 377

Query: 379 VAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQAH 438
           VAPT+  N ++ M IA+EEIFGPVLT + ++  +E IE AN   YGLA  +WT ++K+ H
Sbjct: 378 VAPTLLLNAKNHMRIAQEEIFGPVLTVMTFKDEEEAIELANDINYGLAGYVWTNDIKKGH 437

Query: 439 YIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSVWVNLED 495
            +A R++AG +WVN  NV D  +PFGG K SG+GRE G Y  + YTE K + V++ D
Sbjct: 438 RVAHRVEAGMLWVNAQNVRDLRTPFGGSKYSGIGREGGHYGFEFYTEQKIIHVSISD 494


Lambda     K      H
   0.316    0.133    0.391 

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: 614
Number of extensions: 28
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: 495
Length of database: 502
Length adjustment: 34
Effective length of query: 461
Effective length of database: 468
Effective search space:   215748
Effective search space used:   215748
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: 52 (24.6 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