GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Burkholderia phytofirmans PsJN

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase

Query= reanno::WCS417:GFF827
         (481 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS28770 BPHYT_RS28770 aldehyde
           dehydrogenase
          Length = 480

 Score =  632 bits (1631), Expect = 0.0
 Identities = 312/474 (65%), Positives = 375/474 (79%), Gaps = 1/474 (0%)

Query: 6   RFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQ 65
           +F N++ G+WV G D+  N+NPS+ SDVIG +A+A   Q   AI +AR+AF  WS S  Q
Sbjct: 3   QFKNFVGGEWVDGNDFAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQ 62

Query: 66  ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDY 125
            R D LD+ GS ILAR+ ELG LLAREEGKTL EA+GEV RAG IFKFFAGE LR+ G+ 
Sbjct: 63  QRFDLLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRVGGEI 122

Query: 126 VPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAW 185
           +PSVRPG+ VEVTRE +GV+GLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPG  W
Sbjct: 123 LPSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGSVW 182

Query: 186 ALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQA 245
            L +II+ AG PAGV NLVMG G +VG++LV S  VD +SFTGSVG G+ IA  CV+   
Sbjct: 183 ELVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAIAAKCVATGK 242

Query: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMA 305
           K QLEMGGKNP ++LDDADL  AVE  +  AFYSTGQRCTASSRLIVT+GIHD+FV AM 
Sbjct: 243 KFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHDRFVEAML 302

Query: 306 ERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYL 365
            RM+S+K+G+AL + T IGPVV   QL+QD +YI++ ++EG   V GG  VT  TEG++L
Sbjct: 303 ARMRSLKIGNALDASTQIGPVVDAKQLEQDERYIELARNEGGS-VFGGERVTSATEGFFL 361

Query: 366 APTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425
           AP L  ++  AM I+REE+FGPVA+V++VA+YE ALA+AND+ FGLSAGI T SL +A+H
Sbjct: 362 APALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMSLAHASH 421

Query: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479
           FKRH QAGMVM+N  TAGVDYHVPFGGRKGSS G REQG YA+EFYT+VKT+Y+
Sbjct: 422 FKRHVQAGMVMINTATAGVDYHVPFGGRKGSSLGPREQGTYAREFYTIVKTAYV 475


Lambda     K      H
   0.318    0.134    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: 667
Number of extensions: 15
Number of successful extensions: 2
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: 481
Length of database: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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