GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_068173812.1 HTA01S_RS16360 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_001592305.1:WP_068173812.1
          Length = 483

 Score =  260 bits (665), Expect = 7e-74
 Identities = 163/466 (34%), Positives = 237/466 (50%), Gaps = 21/466 (4%)

Query: 53  VSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRK 112
           VS NP+D  EVV   ++A +   E AI+AAA A   W  +SP+ RA VL +  +++  RK
Sbjct: 26  VSTNPSDTREVVAEYARADRNQTELAIRAAADALPHWSQSSPQRRADVLDQIGSELLARK 85

Query: 113 HEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYTPT 172
            E  ALL +E GK   E   + A A    +++A + + +      + R G +      P 
Sbjct: 86  DELGALLAREEGKTLPEGVGEVARAGQIFKFFAGEALRIPGEVIASVRPGVRVDVTREPV 145

Query: 173 GVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVN 232
           GV  +I PWNF FAI A      +  GNTVV KPA   P       E++   GLP GV N
Sbjct: 146 GVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAEIISRCGLPAGVFN 205

Query: 233 FVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFE----RAAKVQPGQQHLKRVIAEMG 288
            V GSG EVG  LVDHP  + ++FTGS   G RI +    R AKVQ           EMG
Sbjct: 206 LVMGSGREVGQTLVDHPLVNALSFTGSVSTGERILKAATARRAKVQ----------LEMG 255

Query: 289 GKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKV 348
           GK+ +VV  DAD++ A       ++   GQ+C+A SR +V  +V+D  + ++ +   +  
Sbjct: 256 GKNPLVVLADADLDQAVDCALQGSYFSTGQRCTASSRLIVQAQVHDAFVAKLRQRLSTLK 315

Query: 349 TAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGG--TGDDSKGYFIKPTIFAD 405
                     MGPV+D+   ++ ++YIEI + EG   V GG      + G+++ P +F  
Sbjct: 316 VGHALERGTEMGPVVDRAQLEQNLAYIEIARNEGAEHVWGGDLLQRPTPGHYMSPALFL- 374

Query: 406 LDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHV 465
             P+ R+ +EEIFGPV    +  D++ AL +AN+T +GL   + T + K+    K+   V
Sbjct: 375 AKPEHRVAREEIFGPVACVLRADDYEHALVLANDTPFGLCAGICTTSLKYAMHFKRHAEV 434

Query: 466 GNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
           G    N    G  V +H PFGG K S   S+  G   +  +   KT
Sbjct: 435 GMTMVNLPTAG--VDFHVPFGGRKESSHGSREQGRYAVEFYTTVKT 478


Lambda     K      H
   0.316    0.133    0.379 

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: 32
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: 515
Length of database: 483
Length adjustment: 34
Effective length of query: 481
Effective length of database: 449
Effective search space:   215969
Effective search space used:   215969
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 (21.6 bits)
S2: 52 (24.6 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