GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Galbibacter marinus ck-I2-15

Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate WP_008990279.1 I215_RS02025 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q8GAK7
         (458 letters)



>NCBI__GCF_000300875.1:WP_008990279.1
          Length = 455

 Score =  413 bits (1061), Expect = e-120
 Identities = 206/456 (45%), Positives = 298/456 (65%), Gaps = 4/456 (0%)

Query: 3   IATIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEA 62
           +  I+P TG  +  +      +  +++ ++ +AF+  +NTSFE+R+R  +   +  E+  
Sbjct: 4   VTMINPATGEKIDEYIRIDAAQAADKLNKSHSAFKLWKNTSFEQRSRLFNALGNEFENSK 63

Query: 63  DEVARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQF 122
           +  A+L   EMGKT+  A+ E  K A    ++ADHA+ +LS      A E  A   +V F
Sbjct: 64  ERYAQLATQEMGKTIAQARKEIEKCAWICHYYADHAEEFLSNR----AVETEAQKSYVAF 119

Query: 123 DPLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEG 182
            P+GVVLAVMPWN+P +Q +RFAAPA+MAGNTG+LKHASNV  CAL L + F + GFP+G
Sbjct: 120 QPMGVVLAVMPWNFPFYQVIRFAAPAIMAGNTGVLKHASNVQGCALALEEAFRKSGFPDG 179

Query: 183 AFQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVM 242
            F  L +   DV  ++++  + AVTLTGS AAG ++A  AG N+K++V+ELGG D ++++
Sbjct: 180 IFTNLNIGSNDVKGVIENPNVVAVTLTGSDAAGRSVASIAGANLKKTVMELGGSDAYLIL 239

Query: 243 PSADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVAGDPLDES 302
             AD+++A   A + RLQN+GQ+CIAAKRF V ++VY++F  LF   M  A+ GDP +ES
Sbjct: 240 DDADLDQATTLATLGRLQNNGQTCIAAKRFIVQQEVYEKFLELFSKKMEAAIMGDPTEES 299

Query: 303 TSFGPLATERGRQDVHELVRDAREKGAAVQCGGEIPEGEGWYYPATVLTGVTEDMRIYRE 362
           + +GPLA    R ++H+ V  +  +GA +  GG IP+G+G YYPAT+L  VT  M  +  
Sbjct: 300 SYYGPLARIDLRDELHQQVEKSIAQGARLVIGGTIPQGKGAYYPATILADVTPGMEAFDN 359

Query: 363 ECFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIEAGGVFINGLTA 422
           E FGPVA + +    Q AI L+N+S FGL S V T++     + A  ++AG  F+N L  
Sbjct: 360 ELFGPVASVVRAKDEQHAIDLANNSQFGLGSGVITSNNERGEKVALQLQAGSSFVNKLVV 419

Query: 423 SFPAVPFGGLKDSGYGRELSAYGIREFVNIKTVWTS 458
           S P +PFGG+K+SGYGRELS+YGI EFVNIK++W S
Sbjct: 420 SDPRLPFGGIKNSGYGRELSSYGIHEFVNIKSIWIS 455


Lambda     K      H
   0.317    0.132    0.386 

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: 510
Number of extensions: 20
Number of successful extensions: 2
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: 458
Length of database: 455
Length adjustment: 33
Effective length of query: 425
Effective length of database: 422
Effective search space:   179350
Effective search space used:   179350
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: 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