Alignments for a candidate for gabD in Acidovorax caeni R-24608

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabD in Acidovorax caeni R-24608

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_054255048.1 BN2503_RS02410 NAD-dependent succinate-semialdehyde dehydrogenase

Query= reanno::MR1:200453
         (482 letters)



>NCBI__GCF_001298675.1:WP_054255048.1
          Length = 496

 Score =  600 bits (1548), Expect = e-176
 Identities = 304/484 (62%), Positives = 371/484 (76%), Gaps = 7/484 (1%)

Query: 2   LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61
           LL DPSLL+    INGQW   +S+   A+ +PATG  +A V  +G  ET+AAIAAA AA 
Sbjct: 10  LLKDPSLLKTDGLINGQWVAGSSR--FAVHDPATGQRLADVANLGPQETEAAIAAANAAW 67

Query: 62  PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121
           PAWRA T KER A LR+W++LL  N D LA LMT+EQGKPL EA+GEV Y ASF+EWFAE
Sbjct: 68  PAWRAKTVKERSAILRKWYDLLMANQDVLARLMTAEQGKPLPEAQGEVAYGASFVEWFAE 127

Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181
           +AKRI G+T+P    +KR++V++QP+GV AAITPWNFP AMITRK APALAAGC +V+KP
Sbjct: 128 QAKRIDGETLPTFDNNKRLLVLQQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKP 187

Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITGD---AIAIGNEMCTNPIVRKLSFTGSTNVG 238
           A  TP TALA A LA+RAG+P GV +V+T D   ++A+G  +C + +VR LSFTGST VG
Sbjct: 188 AELTPLTALAAAELAQRAGMPPGVLNVVTADSAQSVAVGKALCASDVVRHLSFTGSTEVG 247

Query: 239 IKLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQ 298
             LMAQCAPT+KKLSLELGGNAPFIVFDDA+ID+AVEGA  +KYRNAGQTCVC+NR YVQ
Sbjct: 248 RILMAQCAPTVKKLSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCSNRFYVQ 307

Query: 299 AGVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGG 358
           AGVY+EF  + +  V   KVG G   GV  GPLI  AA++KVQ HL+DA+ KG  V+AGG
Sbjct: 308 AGVYEEFVARFAAKVRTAKVGNGFEPGVNQGPLIEEAALDKVQRHLDDAVAKGGRVVAGG 367

Query: 359 -KVHELG-GNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAA 416
            ++  LG G FFEPTV+ +A  +M  AREETFGP AP+F+F    + +  AN TEFGLA+
Sbjct: 368 QRLSGLGSGQFFEPTVVADATPAMLCAREETFGPFAPIFRFETEQEAVDAANATEFGLAS 427

Query: 417 YFYGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476
           YFY RDI  +++V E+LEYGMVGVNTG+ISTE  PFGG+K SGLGREGS +GI EYLE K
Sbjct: 428 YFYSRDIGRIFRVGEALEYGMVGVNTGIISTEHVPFGGVKQSGLGREGSHHGITEYLETK 487

Query: 477 YICM 480
           Y+C+
Sbjct: 488 YLCV 491


Lambda     K      H
   0.318    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: 698
Number of extensions: 21
Number of successful extensions: 4
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: 482
Length of database: 496
Length adjustment: 34
Effective length of query: 448
Effective length of database: 462
Effective search space:   206976
Effective search space used:   206976
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 24 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 2024 update 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