GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Shewanella loihica PV-4

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= curated2:Q12QD2
         (498 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  215 bits (548), Expect = 2e-60
 Identities = 152/463 (32%), Positives = 226/463 (48%), Gaps = 9/463 (1%)

Query: 13  TQFIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTER 72
           + +I G+W  G+   F  VNPA+ EVI Q + A       AI +A+ A   WS  S  ER
Sbjct: 13  SSYIDGRWTVGE-QRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANER 71

Query: 73  LVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTG-TVE 131
             ++  +   + EH E   R + LE GK L E++ E+      I    +      G T+ 
Sbjct: 72  AALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIP 131

Query: 132 NPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELT 191
            P    +  +  +P GVVA   P+NFP  +       AL AG T + +PS LTP  A   
Sbjct: 132 APANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAM 191

Query: 192 MQLWQQAGLPNGVLNLLQGE--IATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGK 249
            +L ++AG+P GV N++ GE  +  GK L  H  +    FTGS+  G +L  Q A    K
Sbjct: 192 AELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKK 251

Query: 250 ILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKL 309
           + ++E+GGN P I+ + A++DAAV   + S + ++GQ C C  R+F+ K     A   K 
Sbjct: 252 V-SMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGV-AAAFTEKF 309

Query: 310 LTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLGFV 369
             + A + LGD   +     G MIS  A   ++K   D  A+G   +        G  F+
Sbjct: 310 TAAVANLKLGDGLGDGVT-VGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGESFL 368

Query: 370 TPGII-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQH 428
            P I+ DVT+  PLA  E FGP+  +  +     A+  AN+T +GL+A   A        
Sbjct: 369 APVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIGRIFR 428

Query: 429 FYRRIRAGIVNWNKPITGASSAAPFGGIGASGNHRASAYYAAD 471
               +  G+V  N+ I  +++AAPFGG+  SGN R  + Y  D
Sbjct: 429 VAEGLEYGMVGVNEGII-SNAAAPFGGVKQSGNGREGSKYGLD 470


Lambda     K      H
   0.317    0.133    0.390 

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: 511
Number of extensions: 29
Number of successful extensions: 6
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: 498
Length of database: 485
Length adjustment: 34
Effective length of query: 464
Effective length of database: 451
Effective search space:   209264
Effective search space used:   209264
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.

Links

Downloads

Related tools

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