Alignments for a candidate for xacF in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacF in Cereibacter sphaeroides ATCC 17029

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate WP_011842332.1 RSPH17029_RS17095 aldehyde dehydrogenase (NADP(+))

Query= SwissProt::Q08IC0
         (525 letters)



>NCBI__GCF_000015985.1:WP_011842332.1
          Length = 508

 Score =  495 bits (1275), Expect = e-144
 Identities = 275/507 (54%), Positives = 327/507 (64%), Gaps = 13/507 (2%)

Query: 5   GEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRAQPL 64
           G+ LI  E VAG   T    DP+ G    +  F V     V+RAC  A +AF  Y     
Sbjct: 11  GKHLIAGEWVAGE--TSFTSDPAHGP---SHAFSVGTPDLVDRACRAAEEAFWTYGQTTR 65

Query: 65  AARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDGRFL 124
            +RAAFL AIADEI A  +A+ E    ETGLP ARLQGERGRT+GQLRLFA  + +G  L
Sbjct: 66  ESRAAFLRAIADEIEARAEAITEIGRRETGLPEARLQGERGRTIGQLRLFAEHILEGGHL 125

Query: 125 AASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCPVIV 184
               D A P R PLPR D+RL    +GP+ VFGASNFPLAFS AGGDTA+ALAAGCPV+V
Sbjct: 126 DRRHDVALPERQPLPRPDIRLVMRPIGPIAVFGASNFPLAFSTAGGDTAAALAAGCPVVV 185

Query: 185 KAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFTGSR 244
           K H AH GT+E+V  AI AA+ KTGMP GVFSL+ G  R +G ALV HP + AVGFTGS 
Sbjct: 186 KGHGAHPGTAEIVAEAILAAIRKTGMPDGVFSLIQGGRRDVGQALVQHPLIAAVGFTGSL 245

Query: 245 QGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQFCT 304
           +GG AL  +   R  PIP + E+ S+NP+ L P A+ ARG AI  G+  SLT+G GQFCT
Sbjct: 246 KGGRALFDLCAQREVPIPFFGELGSVNPMFLLPEAVKARGAAIGAGWAASLTMGAGQFCT 305

Query: 305 NPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREIGAG 364
           NPG+ +   GP+ D F   AA+AL   PA  MLT  IA AYR GR +    P VR +   
Sbjct: 306 NPGIAVVEIGPEGDAFVAAAAEALRAVPAQCMLTPDIAQAYRKGRSRFDGRPDVRPV--- 362

Query: 365 EAAQTDCQAGGA---LYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQ 421
               TD     A   L+E  A ++L +PA   EVFGP  L+VR    DEV  +   LEGQ
Sbjct: 363 --LTTDSDGRNALPNLFETDAASYLRDPALGEEVFGPLGLVVRVSGADEVDALARGLEGQ 420

Query: 422 LTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTS 481
           LTAT+ MD  D  LA+RL+PVLERKAGRLLVNG+PTGVEV  AMVHGGP+PA++N   TS
Sbjct: 421 LTATIHMDEGDTALAQRLMPVLERKAGRLLVNGFPTGVEVSHAMVHGGPYPASTNFGATS 480

Query: 482 VGATAIERFLRPVCYQDFPDDLLPEGL 508
           VG  +I RFLRPV YQ+ P  LLP  L
Sbjct: 481 VGTLSIRRFLRPVSYQNLPPALLPRDL 507


Lambda     K      H
   0.320    0.137    0.396 

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: 883
Number of extensions: 46
Number of successful extensions: 3
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: 525
Length of database: 508
Length adjustment: 35
Effective length of query: 490
Effective length of database: 473
Effective search space:   231770
Effective search space used:   231770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

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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