GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Halomonas xinjiangensis TRM 0175

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_043532311.1 JH15_RS16505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_000759345.1:WP_043532311.1
          Length = 487

 Score =  241 bits (614), Expect = 5e-68
 Identities = 144/455 (31%), Positives = 240/455 (52%), Gaps = 8/455 (1%)

Query: 6   HLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKRA 65
           ++ G  + AD+G   DVFNP+ GE + +VP   R   ++AI AA AAFPAWR     +RA
Sbjct: 15  YIDGSWVAADSGEQIDVFNPANGEVIGRVPRLGRAETERAITAADAAFPAWRAHTAQERA 74

Query: 66  QVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSRN 125
            +L ++  L+  ++E +  +++ E GK +++AAGE+      + +       + GE    
Sbjct: 75  DILMKWHDLMHEHQEELATIMTLEQGKPLKEAAGEIAYAASFLRWFAEEARRMYGETIPA 134

Query: 126 VGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLIA 185
             PN       QP+GVV  ITP+NFPA +       A+A G   ++KP+ + P S   +A
Sbjct: 135 AKPNQRIVITKQPVGVVGAITPWNFPAAMITRKVGAALAAGCPIVVKPASQTPFSATALA 194

Query: 186 ELFHEAGLPKGVLNVVHGD-KGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQ 244
            L   AG+P+GV NVV G  +    AL E+PEV+ ++F GST +   + S+ ++  +++ 
Sbjct: 195 LLAERAGVPRGVFNVVTGSAREIAAALTESPEVRKITFTGSTEVGRQLMSQASQHIQKIS 254

Query: 245 ALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL-VP 303
              G     ++  DADLD AV   M A + + G+ C+  +    V   + +A  +KL V 
Sbjct: 255 LELGGNAPFIVFEDADLDAAVDGAMAAKFRNGGQTCVCTN-RFLVQSSVVNAFCEKLAVA 313

Query: 304 QIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFF 363
               L++G G    +++GPL+     +KV+ ++   V +GAEL++ G  + + G+    F
Sbjct: 314 MNSELRVGDGLKDDVNIGPLIDADGVEKVSAHVHDAVDKGAELLLGGNPHPLGGN----F 369

Query: 364 LGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAAR 423
              TL +    +M + +EE FGP+  +   +  E+A+ + ND ++G  +  ++RD     
Sbjct: 370 FTPTLVNGANADMLVAQEETFGPLAAVFPFDDEEDAVAMANDTQFGLASYFYSRDLARVW 429

Query: 424 LFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458
              + +E GMVG+N  L +  A   FGG K S  G
Sbjct: 430 RVAESLEYGMVGINTGL-ISNAAAPFGGVKASGLG 463


Lambda     K      H
   0.319    0.137    0.411 

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: 595
Number of extensions: 30
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: 498
Length of database: 487
Length adjustment: 34
Effective length of query: 464
Effective length of database: 453
Effective search space:   210192
Effective search space used:   210192
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 (21.7 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