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_075617829.1 GY23_RS03610 aldehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>NCBI__GCF_001939075.1:WP_075617829.1
          Length = 505

 Score =  412 bits (1058), Expect = e-119
 Identities = 207/472 (43%), Positives = 301/472 (63%), Gaps = 5/472 (1%)

Query: 22  LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81
           L I+G+ V S++G T  T NPATGE +  + +A   D +KAV+AAR +FD G+W+     
Sbjct: 21  LIINGEKVKSSTGETIKTFNPATGELIAEVAKASKEDAEKAVEAARNSFDHGKWKLYPIG 80

Query: 82  SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141
            RS+ + K+A +M     EL +LE LD GK ++    G +  AIE   +YAG      G 
Sbjct: 81  RRSQTLNKIAAIMRARFNELVELEILDTGKSLH-AAQGQVSQAIEDFEFYAGAIVGHRGS 139

Query: 142 TIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSAL 201
              V G + NYT  EPVGV  QIIPWN+PL+MA WK+  A+A GC++++KPA  TPL+A+
Sbjct: 140 VNNVPGQFHNYTEIEPVGVCAQIIPWNYPLMMAAWKIAPAIAVGCSVIVKPASLTPLTAI 199

Query: 202 YLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIK 261
            L E+  +AG PAGV+N+IPG G D G  L  H  V+K+AFTGST IGK IM+ A++++K
Sbjct: 200 ILGEICLEAGVPAGVVNVIPGNGADVGNFLVEHPRVNKVAFTGSTPIGKDIMAKASQTLK 259

Query: 262 RVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMA 321
           RVTLELGGKSP+++  DA++  A+ G+L G+ +N GQ C A SR+++H+D YDE +++  
Sbjct: 260 RVTLELGGKSPSLVFEDADIDAAVDGSLFGIFYNSGQSCEARSRLYVHEDIYDEFMNKFI 319

Query: 322 SYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCP----FEAGY 377
              + L+ G   +K T +G ++ + Q + + SY+Q  K+EGA  + GG       +E G+
Sbjct: 320 EKTKKLQLGNPFNKGTHVGAIIDQGQLDTIDSYVQSAKNEGADILVGGKIAKLEGYENGF 379

Query: 378 FVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQA 437
           +  PT+ ANV   M    +EIFGPV+  + ++   E I  AN SE+GL + +W+++  +A
Sbjct: 380 WYEPTIIANVTHSMKAVTDEIFGPVVVVMKFKDEKEAIRLANDSEFGLGSAVWSKDGARA 439

Query: 438 HYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSV 489
             +A+++QAG V VNC       +PFGGYKQSG GRE+    LD YTE KS+
Sbjct: 440 TRVANQIQAGIVMVNCPFSAFPGTPFGGYKQSGFGRELCIETLDLYTETKSI 491


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: 649
Number of extensions: 35
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: 505
Length adjustment: 34
Effective length of query: 461
Effective length of database: 471
Effective search space:   217131
Effective search space used:   217131
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