GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Coprobacter fastidiosus NSB1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_022599797.1 NSB1T_RS16830 aldehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>NCBI__GCF_000473955.1:WP_022599797.1
          Length = 455

 Score =  145 bits (367), Expect = 2e-39
 Identities = 109/342 (31%), Positives = 164/342 (47%), Gaps = 19/342 (5%)

Query: 144 PVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGV 203
           P GI+ ++SPWN P  LL   +  A+AAGN VI KPS  +  T  +  K++ +A  P  V
Sbjct: 103 PYGISLILSPWNYPFQLLFAPLIGAVAAGNCVILKPSPASPHTTAVSKKIIKEAFDPCHV 162

Query: 204 INIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIF 263
           I I           L+       I +TG     +R+ + ++ H   ++LELGGK+P II 
Sbjct: 163 ILI---EADNRETDLLLQQRYDYIFYTGGVEYGKRVMEAASKHLTPVTLELGGKSPCIID 219

Query: 264 EDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPS 323
           +DAN++      V   F N G+ C+    IFV + I ++ + +  +   + + G     S
Sbjct: 220 KDANIDIAARRIVWGKFLNCGQTCVAPDYIFVHQDIKNDLILKLKDEIIR-QYGKDPQKS 278

Query: 324 ANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDIKD 383
            +   +I        R Y L    +  +I  G   D+  L        ++ PTVI+ I  
Sbjct: 279 PDYPRIIHSG-----RFYNLMLLLKQGKIEAGGKYDEKDL--------YIAPTVISGITP 325

Query: 384 ESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLV 443
           E+R M EEIFGP+  V+ F+  E VI   NS    LA   + K+   I  + +K  SG V
Sbjct: 326 ENRIMNEEIFGPILPVMTFNERETVIDYINSQEKPLALYYFGKNKKNIREILEKTSSGGV 385

Query: 444 WTNCWLIRELN--LPFGGMKSSGIGREGAKDSYDFFTEIKTI 483
             N  +    N  LPFGG+  SGIGR    DS+  F+  K++
Sbjct: 386 CINDVVTHLANPDLPFGGVGHSGIGRYHGIDSFYTFSHTKSV 427


Lambda     K      H
   0.319    0.134    0.404 

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: 491
Number of extensions: 26
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: 487
Length of database: 455
Length adjustment: 33
Effective length of query: 454
Effective length of database: 422
Effective search space:   191588
Effective search space used:   191588
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: 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