GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate AO353_05300 AO353_05300 aldehyde dehydrogenase

Query= metacyc::MONOMER-15203
         (503 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05300
          Length = 481

 Score =  276 bits (706), Expect = 1e-78
 Identities = 170/481 (35%), Positives = 256/481 (53%), Gaps = 9/481 (1%)

Query: 3   IKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDT 62
           +KR +++I G    G A+    +       V G+ A A  A V++A+ AA+AAFPAWS +
Sbjct: 4   VKRFDNFIGGQWVAG-AEYSININPSELSDVIGEYAKADLAQVNAAIDAARAAFPAWSTS 62

Query: 63  PPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLK 122
               R+  + K    + A ++EL   + RE GK   +A GEV+R  +I +F  G    L 
Sbjct: 63  GIQARSDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVSRAGNIFKFFAGECLRLS 122

Query: 123 GDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPS 182
           GDY   V  G++   TR+ LGVV  ITP+NFP+ +P W    A+A GN  VLKP+ L P 
Sbjct: 123 GDYLPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPAELVPG 182

Query: 183 ASLMMADLLKQAGLPDGVFNVVQGDKDSV-EALIDHPDVKALSFVGSTPIANLIYERGAR 241
            +  +A+++ +AG P GVFN+V G    + +A+++ P V  +SF GS  +   I      
Sbjct: 183 CAWALAEIISRAGFPAGVFNLVMGSGRVIGDAMVNSPKVDGISFTGSVGVGRQIAVNCVS 242

Query: 242 SGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVP 301
              ++Q   G KN  +++ DA+L +AV+  + +A+ S G+RC A S  ++   + DK V 
Sbjct: 243 RQAKVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDKFVE 302

Query: 302 RLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTG 361
            +AER + +K+ + L+   ++GP+V+    ++   YI+ G +EGA +V  G      VT 
Sbjct: 303 AMAERMKSIKVGHALKSGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGG----GLVTC 358

Query: 362 EGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCF 421
           +   +G+++  TLF      M I REEIFGPV   VRV D   A+ + ND EFG      
Sbjct: 359 D--TEGYYLAPTLFADSEAAMRISREEIFGPVANIVRVADYDAALAMANDTEFGLSAGIA 416

Query: 422 TESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQK 481
           T S   A  F R  Q GMV +N+P         FGG K S +G +   G     FYT  K
Sbjct: 417 TTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG-SREQGRYAQEFYTVVK 475

Query: 482 S 482
           +
Sbjct: 476 T 476


Lambda     K      H
   0.319    0.136    0.406 

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: 559
Number of extensions: 24
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: 503
Length of database: 481
Length adjustment: 34
Effective length of query: 469
Effective length of database: 447
Effective search space:   209643
Effective search space used:   209643
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