GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Thiohalospira halophila HL 3

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_093427654.1 BM272_RS04975 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_900112605.1:WP_093427654.1
          Length = 454

 Score =  251 bits (642), Expect = 3e-71
 Identities = 153/454 (33%), Positives = 246/454 (54%), Gaps = 7/454 (1%)

Query: 27  VNPAT-EAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASE 85
           ++P+T E      P G+AE    A+ A   A P W A P  ERA  +R I+  +R RA E
Sbjct: 6   IDPSTGETFFHMEPWGEAE-REAALAAVAAATPGWAATPVAERAEAVRAIAGELRRRADE 64

Query: 86  ISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRY-EGEIIQSDRPGENILLFKRALG 144
           ++ LI  E GK+ + A  E+   A   +Y A+    +   E I++D  G++++ ++  LG
Sbjct: 65  LATLITREVGKLHREARGEIEKCAWVCEYYADHGPGFLADEPIETDA-GKSLVAYQ-PLG 122

Query: 145 VTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFNL 204
               ++PWNFPF+ + R  APAL+ GNT V+K +   P +A+A  +++ + GLP   F  
Sbjct: 123 TVLAVMPWNFPFWQVFRFAAPALVAGNTGVLKHASNVPQSALAIEEVIRDAGLPADTFRT 182

Query: 205 VLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDDA 264
           ++ R   V   +  +P++A V++TGS  AG  + + AA NI K  LELGG  P IV+DDA
Sbjct: 183 LMIRAADV-DAVIDDPRIAAVTLTGSEPAGRAVASRAAANIKKAVLELGGSDPFIVLDDA 241

Query: 265 DLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDIA 324
           D+E AV+A   SR +N+GQ C  A+R  +  GI D FV R    ++A+  G+PA      
Sbjct: 242 DVEQAVEAAATSRFLNNGQSCIAAKRFILTPGIADDFVERFRRRVEAMTVGDPAAET-TQ 300

Query: 325 MGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMHEET 384
           +GP+      + +  +VA +V  GA+V  G    +  G +YPP++L  V +      EE 
Sbjct: 301 LGPMARTDLRDELHTQVADSVRAGAQVVTGCTLPDSPGAFYPPSILDHVAEGQRAFEEEL 360

Query: 385 FGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRENFEA 444
           FGPV  V+  D  E A+++AN S +GL  +++T +        + L+ G  ++N      
Sbjct: 361 FGPVAIVLRADDAEHAVNLANGSRFGLGGAVWTADSQRGEAIARRLECGAAFVNGIVKSD 420

Query: 445 MQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478
            +    G + SG G    +HG+ E++  + V+++
Sbjct: 421 PRLPFGGVKASGFGRELSRHGIQEFVNAKTVWVK 454


Lambda     K      H
   0.318    0.135    0.392 

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: 471
Number of extensions: 20
Number of successful extensions: 5
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: 479
Length of database: 454
Length adjustment: 33
Effective length of query: 446
Effective length of database: 421
Effective search space:   187766
Effective search space used:   187766
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