GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Phaeobacter inhibens BS107

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>lcl|FitnessBrowser__Phaeo:GFF501 PGA1_c05130 aldehyde dehydrogenase
          Length = 476

 Score =  258 bits (659), Expect = 3e-73
 Identities = 166/480 (34%), Positives = 251/480 (52%), Gaps = 15/480 (3%)

Query: 36  DYPLVINGERVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPE 95
           +Y  +I G+  ET A   +INP+D ++V+G  + +  E  E+AI AA  A   W  ++P+
Sbjct: 2   EYKNLIAGDWSETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQ 61

Query: 96  ERAAVLFRAAAKVRRRKHEFSALLVKEAGKPWNEADADTAEAIDFMEYYARQMIELAKGK 155
           +R  VL     ++  RK E   LL +E GK   E   + A A    +++A + +  A   
Sbjct: 62  QRFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEI 121

Query: 156 PVNSREGEKNQYVYTPTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAA 215
             + R G   +   +P GV  +I PWNF  AI A      +  G+ VVLKPA  TP  A 
Sbjct: 122 LGSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAH 181

Query: 216 KFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQP 275
              E++  SGLP+GV N V G+G+ VG  LV       I+FTGS E G+ I         
Sbjct: 182 ALAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAAC----- 236

Query: 276 GQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQ 335
           G Q  K++  EMGGK+ +VV +DAD+E A  +    AF   GQ+C+A SR +V E ++D+
Sbjct: 237 GAQR-KKLQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDR 295

Query: 336 VLERVIE-ITESKV-TAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEGRLVSGG--TGD 391
            +  + E +T  +V  A  DS  +  GPV+D+   +K + Y+++   EG  V GG     
Sbjct: 296 FVAALGERMTGLRVGNALDDSTQI--GPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQR 353

Query: 392 DSKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITN 451
            +KG+++ P +  +     R+ QEE+FGP+ +  +V+D+DEAL VAN+T +GL+  + T 
Sbjct: 354 STKGFYLAPALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTG 413

Query: 452 NRKHIERAKQEFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
           + K+    K     G    N    G  V YH PFGG K S   ++  G      + + KT
Sbjct: 414 SLKYATHFKAHAEAGMAMVNLPTAG--VDYHVPFGGTKGSSFGAREQGSHAKEFYTKVKT 471


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: 560
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: 515
Length of database: 476
Length adjustment: 34
Effective length of query: 481
Effective length of database: 442
Effective search space:   212602
Effective search space used:   212602
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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