GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5210745
          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:

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