GapMind for catabolism of small carbon sources

 

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

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-13349
         (490 letters)



>NCBI__GCF_000009985.1:WP_011383257.1
          Length = 499

 Score =  294 bits (753), Expect = 4e-84
 Identities = 177/478 (37%), Positives = 261/478 (54%), Gaps = 12/478 (2%)

Query: 7   YINGEWV--ESARRFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAER 64
           Y++G WV  +  RRFD ++P  G ++A V +        AI A  AA    W + T  +R
Sbjct: 28  YVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN-PWRQRTAKDR 86

Query: 65  AAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPLDTF 124
           AA++    D I    D       A+ GKP+A A   +I  GA+    FA+  K A  D  
Sbjct: 87  AAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMG-EISYGASFISWFAEEGKRAYGDLI 145

Query: 125 QTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGT 184
            T   D  R L   +++P+GVV  ++PWN P+ ++T K APALA G  VV KP+E+TP +
Sbjct: 146 PTTASD--RRL-LVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDTPLS 202

Query: 185 ATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAAT 244
           A  LAE+ H  G+P G+FN+V    P + G  +T N  +  ++FTG +R G  +M   A 
Sbjct: 203 ALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQCAE 262

Query: 245 HVKPVSFELGGKNAAIIFADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLD 304
            VK VS ELGG    I+F DCD +  + G + + + +SGQ C+C  R  V+  IY  F  
Sbjct: 263 TVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYEDFAV 322

Query: 305 AFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDAR 364
              E+  A+ +G    G    GPLI+A    KV ++   A  +GA+VL GG     G   
Sbjct: 323 KLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHALG--- 379

Query: 365 DAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGN 424
             GFW +PT++  +     C +EE FGP+  +  F+TEAEAIALAN +++GL+   ++ +
Sbjct: 380 -GGFW-QPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRD 437

Query: 425 LNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYSELTNVCV 482
           + R  RV+EA+  G+  VN   + +   PFGG+  SG+GREG  + L+ + E   VC+
Sbjct: 438 VARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVCI 495


Lambda     K      H
   0.321    0.137    0.420 

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: 657
Number of extensions: 41
Number of successful extensions: 3
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: 490
Length of database: 499
Length adjustment: 34
Effective length of query: 456
Effective length of database: 465
Effective search space:   212040
Effective search space used:   212040
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