GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Stenotrophomonas chelatiphaga DSM 21508

Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-13349
         (490 letters)



>NCBI__GCF_001431535.1:WP_057507768.1
          Length = 454

 Score =  227 bits (578), Expect = 7e-64
 Identities = 143/461 (31%), Positives = 231/461 (50%), Gaps = 13/461 (2%)

Query: 22  VNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTVAERAAILCRIADEIDRRYDD 81
           VNP  G V  +    D+  ++  ++A   A   AW  T++ ERAA+L  I  ++  R DD
Sbjct: 6   VNPTTGRVDYRHELLDKAGIEQRLQAAAGAFP-AWSATSLQERAAVLRAIGAQLRERKDD 64

Query: 82  FLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPLDTFQTDLPDGARALNYAVRK 141
              A   + GK + + +  ++ + AA    +AD       D  +  L D     +Y   +
Sbjct: 65  IQGAMTREMGK-LKVEALAEVEKCAAACEYYAD----HAADYLKPQLIDTEAQRSYVRYE 119

Query: 142 PLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEETPGTATLLAEVMHTVGVPPGV 201
           P+G V  + PWN P+  +   +APA   GN  + K +   P  A L+ EV+   G+P GV
Sbjct: 120 PIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPDGV 179

Query: 202 FNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRAAATHVKPVSFELGGKNAAII 261
           F+++H    D A + +  +  + A+T TG  R G +I   A   +K    ELGG +A ++
Sbjct: 180 FDVLH-IDNDQAAD-VLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFVV 237

Query: 262 FADCDFEKMIDGMMRAVFLHSGQVCLCAERVYVERPIYNRFLDAFVERVKALKLGWPQDG 321
             D D +K ID  +++ F +SGQ C+ A+R  V   + + F + FV      + G P D 
Sbjct: 238 LDDADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPADA 297

Query: 322 TTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGGGVPKFGDARDAGFWVEPTIITGLPQT 381
            T + P+  A+ RD++    + +  +GA+VL GG   +  D   AG+    T++  +   
Sbjct: 298 RTTLAPMARADLRDELHKQVQASVAKGARVLAGG---EPVDGSHAGY--PATVLDQVGPG 352

Query: 382 ARCIKEEVFGPICHVSPFDTEAEAIALANDTKYGLSATTWTGNLNRGHRVSEAMRVGLSW 441
                EE+FGP+  V     EAEA+ +ANDT++GL  + WT +  RG   ++ M  G ++
Sbjct: 353 MPAYDEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAF 412

Query: 442 VNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYSELTNVCV 482
           VNS    D+R PFGG   SG GRE   H ++ +  +  + V
Sbjct: 413 VNSIVKSDVRLPFGGSKESGFGRELAEHGIHEFMNIKTIYV 453


Lambda     K      H
   0.321    0.137    0.420 

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: 540
Number of extensions: 28
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: 490
Length of database: 454
Length adjustment: 33
Effective length of query: 457
Effective length of database: 421
Effective search space:   192397
Effective search space used:   192397
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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