GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA 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.13237.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: 21.26
//
[ok]

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:

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