Aligments for a candidate for astD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for astD in Herbaspirillum seropedicae SmR1

Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase

Query= curated2:Q12QD2
         (498 letters)



>FitnessBrowser__HerbieS:HSERO_RS05115
          Length = 793

 Score =  207 bits (526), Expect = 1e-57
 Identities = 151/451 (33%), Positives = 230/451 (50%), Gaps = 17/451 (3%)

Query: 15  FIAGQWLAGKGPSFSSVNPANGEVIWQGLGADAGQVDAAITSARAAFYTWSAMSLTERLV 74
           FIAG++   K      ++PA+G+++       A  VDAA+ +A+AA   W A+    R  
Sbjct: 36  FIAGRFTQPKA-DLDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALPGWQALGGHGRAR 94

Query: 75  IVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAERTGTVENPM 134
            + A A  ++ HA L A    L+ GK L ESR     +  +        A+     E+  
Sbjct: 95  HLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQ---ESEF 151

Query: 135 PGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVAELTMQL 194
           P       H P GVV    P+NFP  +    I PAL  GNTV+ KP+E T   A L  +L
Sbjct: 152 PD------HVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTALLFAEL 205

Query: 195 WQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNTGHLLHQQYAGQPGKILALE 254
            QQAGLP GVLN++ G+ ATG A+ +H GI  + FTGS+  G L+ +Q AG  GK L LE
Sbjct: 206 AQQAGLPAGVLNIVTGDGATGAAVVAHPGIQKIAFTGSTEVGRLIREQTAGS-GKSLTLE 264

Query: 255 MGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCTCARRLFIPKTANGDAILAKLLTSTA 314
           +GG +P I+ E A++DAA+  ++ + + + GQ C    RL + +  + D  +A+L T   
Sbjct: 265 LGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIH-DLFIARLKTRMQ 323

Query: 315 KIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQAAGGVSLIELTQVTPGLG-FVTPGI 373
           K+ +G P  +     GA+IS       V++  +     G    ++   TP  G F  P +
Sbjct: 324 KLKVGAPLDKCSD-MGALIS-PVQLERVRSLVEQGVREGAQCHQVVLDTPPGGCFYPPTL 381

Query: 374 I-DVTDASPLADEEHFGPLLKVYRYTDFDAAIDEANNTSFGLSAGLLADSETDYQHFYRR 432
           +  V  A+ +A EE FGP+L    +   D A+  ANN+ +GL+A + +++         +
Sbjct: 382 LTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETIGLALGVAPQ 441

Query: 433 IRAGIVNWNKPITGASSAAPFGGIGASGNHR 463
           ++AG+V W        +A  FGG+  SG  R
Sbjct: 442 LKAGVV-WINSTNQFDAAVGFGGVRESGYGR 471



 Score = 64.7 bits (156), Expect = 1e-14
 Identities = 65/224 (29%), Positives = 96/224 (42%), Gaps = 6/224 (2%)

Query: 11  TQTQFIAGQWLAGKGPSFSSVNPANGEVIWQ-GLGADAGQVDAAITSARAAFYTWSAMSL 69
           T   +I G+ +   G    + +   GE +   GLG      +A   + +A    W++ S 
Sbjct: 517 TAKLYIGGKQVRPDGEVSMACHSTQGERLEDVGLGNRKDIRNAVAAAVKAG--GWTSASP 574

Query: 70  TERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKIAISIKANAER-TG 128
             R   +   AE L    E FAR IA  TG    E+R EV A   ++  +  A A++  G
Sbjct: 575 HRRAQGLYYIAENLSARTEEFARRIASTTGVTADEARAEVDASIKRL-FTYGAWADKFEG 633

Query: 129 TVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVLFKPSELTPKVA 188
            V  P     A    +  GVV V  P   P       + P +  GN V+  PSE  P VA
Sbjct: 634 AVHQPPMRGVALAMPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVA 693

Query: 189 ELTMQLWQQAGLPNGVLNLLQGEIA-TGKALASHKGIDGLFFTG 231
               Q+   + LP GV+N++ G+ A     LA H  ++ L+  G
Sbjct: 694 TDLYQVLDTSDLPAGVINIVTGKSAELLPVLAEHDEVEALWVRG 737


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: 975
Number of extensions: 47
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 498
Length of database: 793
Length adjustment: 38
Effective length of query: 460
Effective length of database: 755
Effective search space:   347300
Effective search space used:   347300
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources