GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Caulobacter crescentus NA1000

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__Caulo:CCNA_03242
          Length = 485

 Score =  277 bits (708), Expect = 7e-79
 Identities = 164/459 (35%), Positives = 246/459 (53%), Gaps = 10/459 (2%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           +P +  +IA V + G AE   A+ AA  AL  AW   +  +R  +L   +D I    DD 
Sbjct: 31  NPADGTLIAAVADLGAAETTLAIDAAHRALP-AWAARTAKERGAILRRWSDLILAHADDL 89

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
                ++ GKP++ A+  ++  GA+    FA+  K         P P   G    ++++P
Sbjct: 90  ARLMTDEQGKPLAEAKG-EVVYGASFIDWFAEEAKRAYGHTIPTPMP---GKRLASIKQP 145

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
           VGV   I PWN P+ ++T KVGPALA G TVVVKP+ ETP +A  +  +   AGVP GV 
Sbjct: 146 VGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSALAIARLATEAGVPAGVL 205

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           N+V     +  G+ L     V  ++FTG T  G+ + +  A   + +SLELGG    IVF
Sbjct: 206 NIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKKLSLELGGNAPFIVF 265

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
            D DL+ A++G + S + N GQ C+   R+ V+  I D F +RL +    +++G      
Sbjct: 266 DDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAARLAEKVAALKVGPGTGEG 325

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
             +GPLI+++   KV+     AV+AGA V+TGG V  +     GG + QPT+  G   + 
Sbjct: 326 VQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGL-----GGHFYQPTVLVGATPEM 380

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            + +EEIFGP A ++ F++E E +  AN   +GLA   ++ ++ R  RVA  IE G+  +
Sbjct: 381 RIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRCWRVAEQIEAGMVGI 440

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVC 482
           N   +      FGG K+SG+GREG    L+ Y E K +C
Sbjct: 441 NEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLC 479


Lambda     K      H
   0.318    0.135    0.406 

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: 561
Number of extensions: 20
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: 485
Length of database: 485
Length adjustment: 34
Effective length of query: 451
Effective length of database: 451
Effective search space:   203401
Effective search space used:   203401
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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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