Alignments for a candidate for putA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Desulfovibrio vulgaris Hildenborough

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 208845 DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>MicrobesOnline__882:208845
          Length = 1006

 Score =  486 bits (1251), Expect = e-141
 Identities = 247/512 (48%), Positives = 325/512 (63%)

Query: 2   LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61
           L P+ ++   DFTV  NRKAF EAL  V    G+  PL I G  VTT D I + NPA+  
Sbjct: 477 LPPFTNDAMIDFTVPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPA 536

Query: 62  QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121
           ++V S+ +A +   + AI +A +A  TWR+ +P +RA  L +AA I R+R  E SAW V 
Sbjct: 537 EVVASICQAGRPEIDDAIAAAKKAALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVV 596

Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181
           E GK W +A  D  E IDFLEYYAR+M+ L   + +   PGE N  FY P G+   I+PW
Sbjct: 597 EVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEHNHLFYQPKGIAAVIAPW 656

Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241
           NF  AI +G A A IVTGN V+ KP+S +  +     EV  +AGLP+GV NY PG  + +
Sbjct: 657 NFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIM 716

Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301
           GDYLV+HP  SLI FTGS +VG+R+ E+AA V+PGQ   KRVI EMGGK+  ++D DADL
Sbjct: 717 GDYLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADL 776

Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361
           D A   +L SAFGF GQKCSA SR ++   +YD  +E+ V  A ++ +G   +  NYMGP
Sbjct: 777 DEAVLQVLYSAFGFQGQKCSACSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGP 836

Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421
           V D    + +  YI I ++EGR++       + G ++  TI+ D+ PE  I QEEIFGPV
Sbjct: 837 VADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLTIVGDIRPEHRIAQEEIFGPV 896

Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481
           +A  +A  FD AL IAN T + LTGAV +R+  H+++A+REF VGNLY N+  TGA+V  
Sbjct: 897 LAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVER 956

Query: 482 HPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
            PFGGF MSG  SK GGPDYL   M  + V+E
Sbjct: 957 QPFGGFAMSGVGSKTGGPDYLLQFMDPRVVTE 988


Lambda     K      H
   0.316    0.134    0.388 

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: 1188
Number of extensions: 45
Number of successful extensions: 1
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: 1006
Length adjustment: 40
Effective length of query: 475
Effective length of database: 966
Effective search space:   458850
Effective search space used:   458850
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: 55 (25.8 bits)

Align candidate 208845 DVU3319 (proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01237 (pruA: putative delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01237.hmm
# target sequence database:        /tmp/gapView.21185.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01237  [M=511]
Accession:   TIGR01237
Description: D1pyr5carbox2: putative delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-204  666.7   0.0   1.6e-204  666.4   0.0    1.1  1  lcl|MicrobesOnline__882:208845  DVU3319 proline dehydrogenase/de


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208845  DVU3319 proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.4   0.0  1.6e-204  1.6e-204       3     510 ..     482     989 ..     480     990 .. 0.99

  Alignments for each domain:
  == domain 1  score: 666.4 bits;  conditional E-value: 1.6e-204
                       TIGR01237   3 nepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeqalqaakka 81 
                                     n+   df+  ++++af +ala v+  +G++ pl+i G+ v t++ i + npa++ evv  +++a   + ++a+ aakka
  lcl|MicrobesOnline__882:208845 482 NDAMIDFTVPDNRKAFVEALADVRSRFGQTVPLYIGGRDVTTADLIPTTNPAKPAEVVASICQAGRPEIDDAIAAAKKA 560
                                     67788************************************************************************** PP

                       TIGR01237  82 feewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremiklakskevlsieGek 160
                                       +w+ t++ +raa l++aa+i ++r  elsa+ v+evGk++++a  +v+e idfleyyarem++l   +     +Ge+
  lcl|MicrobesOnline__882:208845 561 ALTWRDTSPADRAAYLRRAADICRKRIWELSAWQVVEVGKQWDQAYHDVTEGIDFLEYYAREMLRLGAPRRMGRAPGEH 639
                                     ******************************************************************************* PP

                       TIGR01237 161 nrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveileeaGlpkGvlqfvpGkGsevGe 239
                                     n+++y+p+G+a vi+pwnfp+ai++Gm+ a+ivtGn v+ kp++ ++ i   l+e+++eaGlp+Gv+++ pG+ s +G+
  lcl|MicrobesOnline__882:208845 640 NHLFYQPKGIAAVIAPWNFPFAIAIGMASAAIVTGNPVIFKPSSISSRIGYNLAEVFREAGLPEGVFNYCPGRSSIMGD 718
                                     ******************************************************************************* PP

                       TIGR01237 240 ylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivdesadieqavaaavtsafGfaGqkcsa 318
                                     ylv+hp+++li+ftGs evGlri e+aakvqpGq+  krviae+GGk+a i+d++ad+++av  +++safGf+Gqkcsa
  lcl|MicrobesOnline__882:208845 719 YLVEHPDISLICFTGSMEVGLRIQEKAAKVQPGQRQCKRVIAEMGGKNATIIDDDADLDEAVLQVLYSAFGFQGQKCSA 797
                                     ******************************************************************************* PP

                       TIGR01237 319 asrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikpt 397
                                     +srv+vl+ +yd+++er+v+a+ s ++g++++++ ++gpv d++ ++++ +yi ++++eg+++l  +d + +G ++  t
  lcl|MicrobesOnline__882:208845 798 CSRVIVLDAIYDRFIERLVKAASSIHIGPSEDPSNYMGPVADATLQKNVSDYIRIAEEEGRVLLKRTDLPAEGCYVPLT 876
                                     ******************************************************************************* PP

                       TIGR01237 398 ifkdvdrkarlaqeeifGpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivg 476
                                     i++d+ ++ r+aqeeifGpv+av+ra+ fdeal ian+t ++ltG+v+s+s+e++++a+ ef+vGnly+n+  tGa+v 
  lcl|MicrobesOnline__882:208845 877 IVGDIRPEHRIAQEEIFGPVLAVMRAATFDEALSIANGTRFALTGAVFSRSPEHLDKARREFRVGNLYLNKGSTGALVE 955
                                     ******************************************************************************* PP

                       TIGR01237 477 vqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                     +qpfGGf msG++sk+GGpdyl+qf++++ vte+
  lcl|MicrobesOnline__882:208845 956 RQPFGGFAMSGVGSKTGGPDYLLQFMDPRVVTEN 989
                                     ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (1006 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 15.20
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources