GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Shewanella loihica PV-4

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__PV4:5210745 Shew_3173 succinic semialdehyde
           dehydrogenase (RefSeq)
          Length = 485

 Score =  340 bits (872), Expect = 6e-98
 Identities = 189/473 (39%), Positives = 265/473 (56%), Gaps = 8/473 (1%)

Query: 8   DTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW 62
           DTQL+     IDG W      +  DVVNPA+ + I +V  A + D   A+ AA+     W
Sbjct: 6   DTQLIKLSSYIDGRWT--VGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEW 63

Query: 63  RKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGR 122
            K  A+ERAA MRK   L+ E  + + +L+T EQGKPL EA+ E+   A  I+WFA+EG+
Sbjct: 64  SKRSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGK 123

Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182
           RVYG  +P      +  V+K+PVG VA+ TPWNFP   + RK +AALA GC+F+ +    
Sbjct: 124 RVYGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPL 183

Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAE-ISSYLIPHPVIRKVTFTGSTPVGKQLAS 241
           TP S  A+      AG+PAGV  +V G+ A  +   L  HP + K TFTGST VGK L +
Sbjct: 184 TPLSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLA 243

Query: 242 LAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRD 301
                +K+ +MELGG+AP IV +DAD+  AV+ A  +K+RNAGQ C+   R  V   +  
Sbjct: 244 QCATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAA 303

Query: 302 EFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGS 361
            FT         LK+G+GL +G T+G + +   +  +  ++D+    GA + TGG+    
Sbjct: 304 AFTEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSEL 363

Query: 362 EGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSF 421
             +F AP ++ +V  +  +  NE FGPV  I  FD   EA+A AN   +GLA Y + R  
Sbjct: 364 GESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDI 423

Query: 422 ANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
             +  + + LE GM+ +N+        PFGGVK SG G EG    L+ YL  K
Sbjct: 424 GRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIK 476


Lambda     K      H
   0.318    0.134    0.393 

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: 627
Number of extensions: 29
Number of successful extensions: 2
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: 481
Length of database: 485
Length adjustment: 34
Effective length of query: 447
Effective length of database: 451
Effective search space:   201597
Effective search space used:   201597
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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