Alignments for a candidate for rocA in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Desulfovibrio vulgaris Miyazaki F

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 8501416 DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= BRENDA::Q9K9B2
         (515 letters)



>FitnessBrowser__Miya:8501416
          Length = 1013

 Score =  477 bits (1228), Expect = e-139
 Identities = 236/512 (46%), Positives = 324/512 (63%)

Query: 2   LQPYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKD 61
           L P+ +E   D T+ ANR  F  A+  V  + G   PL I G+ VTT+D I S NPA+  
Sbjct: 484 LPPFVNESMLDLTIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPAKPA 543

Query: 62  QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121
           +++  V +  +   + AI++A +AF  WR+ +P +RA  L +AA I RRR  E SAW V 
Sbjct: 544 EVIARVCQGGKPEVDAAIEAAQKAFPAWRDTSPADRAMFLHRAADIARRRMFELSAWQVL 603

Query: 122 EAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPW 181
           E GK W +A  D  E IDFL+YYA +M+ L   + +   PGE N  FY P G+   I+PW
Sbjct: 604 EVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHLFYQPKGIAAVIAPW 663

Query: 182 NFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEV 241
           NF  AI +G A A IVTGN V+ KP+S    +     E+  +AGLP+GV NYVPG  + +
Sbjct: 664 NFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVM 723

Query: 242 GDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADL 301
           GDYLV+HP+ S+I FTGS +VG+R+ E+AA V+PGQ   KRVI EMGGK+ +++D DADL
Sbjct: 724 GDYLVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADL 783

Query: 302 DLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGP 361
           D A   +L SAFGF GQKCSA SR ++   +YD  +E+ V  A+ + +G   +  NYMGP
Sbjct: 784 DEAVLQVLYSAFGFQGQKCSACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGP 843

Query: 362 VIDEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPV 421
           V D    + I+ Y+++ ++EG+++       + G ++  TI+  + P   I QEEIFGPV
Sbjct: 844 VADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYVPLTIVEGIKPHHRIAQEEIFGPV 903

Query: 422 VAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGY 481
           +A  +A +FD AL IAN T + LTG V +R+  ++ +A+REF VGNLY NR  TGA+V  
Sbjct: 904 LAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGSTGAMVER 963

Query: 482 HPFGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
            PFGGFKMSG  SK GGPDYL   M  + V+E
Sbjct: 964 QPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTE 995


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: 1189
Number of extensions: 50
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: 1013
Length adjustment: 40
Effective length of query: 475
Effective length of database: 973
Effective search space:   462175
Effective search space used:   462175
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 8501416 DvMF_2146 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.6786.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.7e-204  666.2   0.0   2.2e-204  665.9   0.0    1.1  1  lcl|FitnessBrowser__Miya:8501416  DvMF_2146 delta-1-pyrroline-5-ca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501416  DvMF_2146 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.9   0.0  2.2e-204  2.2e-204      10     510 ..     496     996 ..     487     997 .. 0.99

  Alignments for each domain:
  == domain 1  score: 665.9 bits;  conditional E-value: 2.2e-204
                         TIGR01237  10 adeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeqalqaakkafeewk 86 
                                       +   ++  f +a+a+v+ + G   pl+i G+ v t++ i s npa++ ev+ +v++    + + a++aa+kaf++w+
  lcl|FitnessBrowser__Miya:8501416 496 TIPANRAGFVNAIAEVRGKAGGVIPLFIGGKDVTTDDTIASTNPAKPAEVIARVCQGGKPEVDAAIEAAQKAFPAWR 572
                                       5556788899******************************************************************* PP

                         TIGR01237  87 ktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremiklakskevlsieGeknry 163
                                        t++ +ra  l +aa+i +rr +elsa+ vlevGk++++a  +v e idfl+yya+em++l   +     +Ge n++
  lcl|FitnessBrowser__Miya:8501416 573 DTSPADRAMFLHRAADIARRRMFELSAWQVLEVGKQWDQAFHDVGEGIDFLDYYAHEMLRLGTPRRMGRAPGELNHL 649
                                       ***************************************************************************** PP

                         TIGR01237 164 lyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveileeaGlpkGvlqfvpGkGsevGey 240
                                       +y+p+G+a vi+pwnfp+ai++Gm++a+ivtGn v+ kp++ a+ i   l ei++eaGlp+Gv+++vpG+ s++G+y
  lcl|FitnessBrowser__Miya:8501416 650 FYQPKGIAAVIAPWNFPFAIAIGMAAAAIVTGNPVIFKPSSIASRIGYNLTEIFREAGLPEGVFNYVPGRSSVMGDY 726
                                       ***************************************************************************** PP

                         TIGR01237 241 lvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivdesadieqavaaavtsafGfaGqkcs 317
                                       lv+hp++++i+ftGs evGlri e+aakvqpGq   krviae+GGk+a+i+d++ad+++av  +++safGf+Gqkcs
  lcl|FitnessBrowser__Miya:8501416 727 LVEHPQVSMICFTGSMEVGLRIQEKAAKVQPGQMQCKRVIAEMGGKNAIIIDDDADLDEAVLQVLYSAFGFQGQKCS 803
                                       ***************************************************************************** PP

                         TIGR01237 318 aasrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfi 394
                                       a+srv+vl+++yd++ver+v+a+++ k+g+++++  ++gpv d+  +++i ey++++++egk+++  +d + +G ++
  lcl|FitnessBrowser__Miya:8501416 804 ACSRVIVLDPIYDRFVERLVKAAQAIKIGPSEDPANYMGPVADASLQKNILEYVKVAEQEGKVLVKRTDIPAEGCYV 880
                                       ***************************************************************************** PP

                         TIGR01237 395 kptifkdvdrkarlaqeeifGpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkit 471
                                         ti++ + ++ r+aqeeifGpv+av+ra +fdeal ian+t ++ltGgv+s+s+e++ +a+ ef+vGnly+nr  t
  lcl|FitnessBrowser__Miya:8501416 881 PLTIVEGIKPHHRIAQEEIFGPVLAVMRAGNFDEALAIANGTRFALTGGVFSRSPENLTKARREFRVGNLYLNRGST 957
                                       ***************************************************************************** PP

                         TIGR01237 472 GaivgvqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                       Ga+v +qpfGGfkmsG++sk+GGpdyl+qf++++ vte+
  lcl|FitnessBrowser__Miya:8501416 958 GAMVERQPFGGFKMSGVGSKTGGPDYLLQFMDPRCVTEN 996
                                       *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (1013 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 18.87
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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