Alignments for a candidate for davD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Herbaspirillum seropedicae SmR1

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate HSERO_RS05395 HSERO_RS05395 succinate-semialdehyde dehdyrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__HerbieS:HSERO_RS05395
          Length = 484

 Score =  708 bits (1828), Expect = 0.0
 Identities = 346/483 (71%), Positives = 405/483 (83%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           +QLKD  L RQQA+V+G W DAD G+ + V+NPA GE++G VP MGAAETRRAIEAA+ A
Sbjct: 2   LQLKDPALLRQQAFVNGQWCDADQGERLAVHNPANGELLGHVPLMGAAETRRAIEAANAA 61

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
            PAW+  TAKER+  LRRW++LM+ N DDLA +MT EQGKPLAEA+GEI YAASF+EWF 
Sbjct: 62  WPAWKKKTAKERSAILRRWYELMLANTDDLALIMTAEQGKPLAEARGEIGYAASFIEWFA 121

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EE KR YGDTIP   P  RI+VIK+ IGV AAITPWNFP+AMITRKAGPALAAGC MVLK
Sbjct: 122 EEGKRTYGDTIPSPSPSNRIVVIKEAIGVCAAITPWNFPAAMITRKAGPALAAGCPMVLK 181

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           PA  TP+SALALA LAERAGIP GVFSVVTG+   +GGE+TSNPIVRK++FTGST +G+ 
Sbjct: 182 PAEATPFSALALAVLAERAGIPAGVFSVVTGTPKGIGGEMTSNPIVRKISFTGSTGVGKL 241

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           LM + A  IKK+SLELGGNAPFIVFDDADLDAAVEGA+ SKYRN GQTCVCANR+YVQDG
Sbjct: 242 LMQQSASSIKKLSLELGGNAPFIVFDDADLDAAVEGAIASKYRNAGQTCVCANRIYVQDG 301

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYDAF  KL  AV K  +G G E GVT GPLI+ +AV KVE+H+ADAV+KGA+V+ GGK 
Sbjct: 302 VYDAFAAKLVEAVKKFKVGQGTEEGVTQGPLINEQAVQKVEQHVADAVAKGARVLLGGKR 361

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           HALG +FFEPT+L DV     V+++ETFGP+AP+FRFK + EV+A++NDTEFGLASYFY+
Sbjct: 362 HALGHSFFEPTVLADVTPAMQVAREETFGPMAPLFRFKTDEEVLALANDTEFGLASYFYS 421

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           RD+ R++RVAE LE GMVGINTGLISNEVAPFGG+K SGLGREGS YGI+DYL +KYLC+
Sbjct: 422 RDIGRIWRVAEGLESGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYLVVKYLCM 481

Query: 481 GGI 483
           GGI
Sbjct: 482 GGI 484


Lambda     K      H
   0.317    0.135    0.391 

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: 689
Number of extensions: 11
Number of successful extensions: 1
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: 483
Length of database: 484
Length adjustment: 34
Effective length of query: 449
Effective length of database: 450
Effective search space:   202050
Effective search space used:   202050
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

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
the source code
instructions for running GapMind on your computer

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