GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Magnetospirillum magneticum AMB-1

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  211 bits (537), Expect = 5e-59
 Identities = 141/456 (30%), Positives = 228/456 (50%), Gaps = 11/456 (2%)

Query: 10  YIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRRS 69
           Y+DG    +D+ R  +V +PATG + A V     +    A+ +A AA+  W ++++  R+
Sbjct: 28  YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPWRQRTAKDRA 87

Query: 70  RVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSDN 129
            VM  + +L+  H D LA+++S E GK L++A GE++ G   + +          D    
Sbjct: 88  AVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGKRAYGDLIPT 147

Query: 130 IGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLMA 189
                    ++QP+GV A VTP+NFP+ +       AL AG   ++KP+E  P ++L +A
Sbjct: 148 TASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 207

Query: 190 RLLTEAGLPDGVFNVVQGDKVAV--DALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKRV 247
            L   AGLP G+FN+V   + A     +  +  +  +SF GST + + +  Q     K+V
Sbjct: 208 ELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAETVKKV 267

Query: 248 QALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPR 307
               G     IV  D DLD A    + + Y ++G+ C+  +  +    + ++   KL  +
Sbjct: 268 SLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAVKLAEK 327

Query: 308 IDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFFV 367
              + +G+        GPL+ A   AKV   +   V++GAR++  GR    P A  G F 
Sbjct: 328 AAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGR----PHALGGGFW 383

Query: 368 GATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARA 427
             T+   VT  M  +++E FGPV  ++R    A A+AL NA EFG     ++RD  +AR 
Sbjct: 384 QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRD--VARV 441

Query: 428 F--ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFG 461
           F  A +++ GMVG+N  + +      FGG K S  G
Sbjct: 442 FRVAEALECGMVGVNESL-ISNEVAPFGGIKESGLG 476


Lambda     K      H
   0.320    0.137    0.412 

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: 553
Number of extensions: 27
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: 500
Length of database: 499
Length adjustment: 34
Effective length of query: 466
Effective length of database: 465
Effective search space:   216690
Effective search space used:   216690
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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