Alignments for a candidate for davD in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Cereibacter sphaeroides ATCC 17029

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_000015985.1:WP_011842384.1
          Length = 791

 Score =  298 bits (764), Expect = 4e-85
 Identities = 171/462 (37%), Positives = 259/462 (56%), Gaps = 16/462 (3%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           Y+DGA+  A+    I+V NPATGEI+  +P  G AE   A+ AA  A   W  L   ERA
Sbjct: 36  YIDGAFTGAETA-AIEVENPATGEILARIPAAGEAEIEAAVAAARAAFSGWSQLPGFERA 94

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAK-GEIAYAAS-FLEWFGEEAKRIYGDTI 131
             L      + + +   + L T++ GK + E +  ++  A   F    G  A  + G+  
Sbjct: 95  RYLYAIARGLQKRERFFSVLETLDNGKAIRETRTADVPLAIRHFYHHAGWAA--VLGEEF 152

Query: 132 PGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALA 191
           PGH+P          +GV   + PWNFP  M+  K  PALAAG T+VLKPA  TP +A+A
Sbjct: 153 PGHEP----------LGVCGQVIPWNFPMLMLAWKIAPALAAGNTVVLKPADLTPLTAVA 202

Query: 192 LAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKK 251
            AE+ +  G+P+GV ++V G A E G  L  +P V K+ FTGST +GR++    A   K 
Sbjct: 203 FAEMLDEIGLPRGVVNIVHGGA-ETGALLVRHPGVAKVAFTGSTAVGREIRRATAGSGKS 261

Query: 252 VSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKA 311
           ++LELGG +PF+V  DADLDAAVEG +   + N G+ C   +RL +Q+G+ + F+ KL+A
Sbjct: 262 LTLELGGKSPFVVCADADLDAAVEGVVEGVWFNQGEVCCAGSRLLLQEGIAERFLAKLRA 321

Query: 312 AVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPT 371
            + K+ +G+ L+     G ++ A+  A++EE IA A  +G ++     P    G F  P 
Sbjct: 322 RMEKIRVGDPLDKSTDMGAIVSARQKARIEELIAGAAREGYRLEQAACPLPAAGHFVAPG 381

Query: 372 ILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAE 431
              D    A V++ E FGP+A    F+   E +A++N+T +GLA+  ++ ++     +A 
Sbjct: 382 FFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALANNTPYGLAASVWSENINAATELAA 441

Query: 432 QLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYL 473
           ++  G+V IN   + +  A FGG+K SG GREG++ G+  YL
Sbjct: 442 RIRAGVVWINASNLFDAGASFGGMKESGFGREGAREGLGAYL 483



 Score = 76.6 bits (187), Expect = 3e-18
 Identities = 65/239 (27%), Positives = 109/239 (45%), Gaps = 5/239 (2%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           Y+ GA V  D G +  V  P  GE +G  P  G  + R A+EAA KA   W A  A  RA
Sbjct: 521 YIGGAQVRPDGGASYVVRGPK-GEALGLAPVSGRKDIRNAVEAALKA-KGWAA-NAHGRA 577

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133
             L    + +    +DLA  + ++ G   +EA  E+      + ++   A +  G  I  
Sbjct: 578 QVLFFLAENIAARAEDLAAAL-VQGGAGRSEAAAEVRSLIERVFFYAGMADKDDG-RIHA 635

Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193
            +P    + +K+P+GV   + P   P   +     P +AAG  +V  P+      A  L 
Sbjct: 636 TKPRHLTLSVKEPLGVVGVLAPDEAPLLSLMSLILPLIAAGNRVVAVPSPAQALLAQPLT 695

Query: 194 ELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252
           ++ + + +P GV ++VTG    +   L  +  V  + + GS +   ++ A  A ++K+V
Sbjct: 696 QIFDTSDLPGGVVNLVTGDRNLLARTLAEHDAVDGIWYHGSAKGAAEVEALSAGNLKQV 754


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: 910
Number of extensions: 50
Number of successful extensions: 4
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: 483
Length of database: 791
Length adjustment: 37
Effective length of query: 446
Effective length of database: 754
Effective search space:   336284
Effective search space used:   336284
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: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. 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:

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