Alignments for a candidate for putA in Salinicoccus carnicancri Crm

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Salinicoccus carnicancri Crm

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_017547991.1 C792_RS0103150 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>NCBI__GCF_000330705.1:WP_017547991.1
          Length = 513

 Score =  663 bits (1711), Expect = 0.0
 Identities = 320/510 (62%), Positives = 402/510 (78%), Gaps = 1/510 (0%)

Query: 4   PYKHEPFTDFTVEANRKAFEEALGLVEKELGKEYPLIINGERVTTEDKIQSWNPARKDQL 63
           PYKHEPFTDF++E NR   +E L  V+  LGK+YPLII GER+ T++K +S+NP+ K ++
Sbjct: 3   PYKHEPFTDFSIEENRTKLQEGLKTVKSYLGKDYPLIIGGERIMTDEKKESYNPSEKTEM 62

Query: 64  VGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEA 123
           +G +S+ANQ+ A++A+ +A E F++WR    E R+++L KAAAIIR+RK EF+A LV EA
Sbjct: 63  IGHMSQANQEHAQRAMDAALETFESWRKSTFEFRSDVLFKAAAIIRKRKFEFTALLVKEA 122

Query: 124 GKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNF 183
           GKPWKEADADTAEAIDFLEYY R  +++  G  + SRPGE N++ Y P+GV + ISPWNF
Sbjct: 123 GKPWKEADADTAEAIDFLEYYGRNNLKIKDGDHVESRPGEYNQFHYIPLGVGLVISPWNF 182

Query: 184 ALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGD 243
           A AIM GT  A +VTGNTV+LKP+S TP+VA KF+EVLE+AG+PKG +N++PGS  ++GD
Sbjct: 183 AFAIMAGTTAAALVTGNTVLLKPSSRTPIVAYKFMEVLEEAGMPKGAVNFIPGSSRDIGD 242

Query: 244 YLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDTVVVDRDADLDL 303
           YLV+H  T  ++FTGS+DVG R+YE+AA+V+ GQ HLKRVI EMGGKDT+VVD DADL+L
Sbjct: 243 YLVEHKDTRFVSFTGSRDVGTRIYEKAAIVQDGQTHLKRVIAEMGGKDTIVVDSDADLEL 302

Query: 304 AAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVI 363
           AAE+I  SAFGFSGQKCSA SR +  +D++DE+L K V   + L VG+P + D  +GPVI
Sbjct: 303 AAEAITYSAFGFSGQKCSACSRVIALEDIHDELLAKVVEKTRQLKVGNPES-DVNVGPVI 361

Query: 364 DEKAFEKIMSYIEIGKKEGRLMTGGEGDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVA 423
           D+ + EKI  YIEIGK EG+L TGG  ++ TG F+ PTI + L  +  IMQEEIFGPVV 
Sbjct: 362 DDASLEKIGKYIEIGKSEGKLETGGTTENDTGHFVHPTIFSGLRHDDRIMQEEIFGPVVG 421

Query: 424 FSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHP 483
           F+ A DFD A+E AN T+YGLTGAVIT+NR HIEQA+R+F VGNLYFNR CT AIVGY P
Sbjct: 422 FATAKDFDQAIEYANATDYGLTGAVITQNREHIEQARRDFMVGNLYFNRGCTAAIVGYQP 481

Query: 484 FGGFKMSGTDSKAGGPDYLALHMQAKTVSE 513
           FGGFKMSGTDSKAGGPDYL LHMQ KT SE
Sbjct: 482 FGGFKMSGTDSKAGGPDYLTLHMQGKTSSE 511


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: 854
Number of extensions: 29
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: 515
Length of database: 513
Length adjustment: 35
Effective length of query: 480
Effective length of database: 478
Effective search space:   229440
Effective search space used:   229440
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)

Align candidate WP_017547991.1 C792_RS0103150 (L-glutamate gamma-semialdehyde 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.2496075.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.2e-234  763.6   0.2   5.8e-234  763.5   0.2    1.0  1  NCBI__GCF_000330705.1:WP_017547991.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330705.1:WP_017547991.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  763.5   0.2  5.8e-234  5.8e-234       1     510 [.       4     512 ..       4     513 .] 1.00

  Alignments for each domain:
  == domain 1  score: 763.5 bits;  conditional E-value: 5.8e-234
                             TIGR01237   1 yknepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeq 73 
                                           yk+epftdf+ ee++ + ++ l +vk +lGkdypl+i Ge++ t++k +s np++k e++G++++a +e+a++
  NCBI__GCF_000330705.1:WP_017547991.1   4 YKHEPFTDFSIEENRTKLQEGLKTVKSYLGKDYPLIIGGERIMTDEKKESYNPSEKTEMIGHMSQANQEHAQR 76 
                                           9************************************************************************ PP

                             TIGR01237  74 alqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremik 146
                                           a++aa ++fe+w+k   e r+ +l+kaaai+++r++e++allv+e+Gk+++eada++aeaidfleyy r+ +k
  NCBI__GCF_000330705.1:WP_017547991.1  77 AMDAALETFESWRKSTFEFRSDVLFKAAAIIRKRKFEFTALLVKEAGKPWKEADADTAEAIDFLEYYGRNNLK 149
                                           ************************************************************************* PP

                             TIGR01237 147 lakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveilee 219
                                           ++++++v s++Ge n++ yiplGv++vispwnf +ai++G+t+a++vtGn+v+lkp++ ++++a k++e+lee
  NCBI__GCF_000330705.1:WP_017547991.1 150 IKDGDHVESRPGEYNQFHYIPLGVGLVISPWNFAFAIMAGTTAAALVTGNTVLLKPSSRTPIVAYKFMEVLEE 222
                                           ************************************************************************* PP

                             TIGR01237 220 aGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivd 292
                                           aG+pkG ++f+pG+ +++G+ylv+h +tr+++ftGsr+vG+riye+aa vq Gq hlkrviae+GGkd+++vd
  NCBI__GCF_000330705.1:WP_017547991.1 223 AGMPKGAVNFIPGSSRDIGDYLVEHKDTRFVSFTGSRDVGTRIYEKAAIVQDGQTHLKRVIAEMGGKDTIVVD 295
                                           ************************************************************************* PP

                             TIGR01237 293 esadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfd 365
                                            +ad+e a++a+++safGf+Gqkcsa+srv+ le+++de++ ++ve+t+ lkvg++++ dv+vgpvid+ s +
  NCBI__GCF_000330705.1:WP_017547991.1 296 SDADLELAAEAITYSAFGFSGQKCSACSRVIALEDIHDELLAKVVEKTRQLKVGNPES-DVNVGPVIDDASLE 367
                                           *********************************************************9.************** PP

                             TIGR01237 366 kikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGpvvavlrakdfdealeianstey 438
                                           ki +yie+gk+egkl  gg+++++ G+f++ptif+ + ++ r++qeeifGpvv +  akdfd+a+e an+t+y
  NCBI__GCF_000330705.1:WP_017547991.1 368 KIGKYIEIGKSEGKLETGGTTENDTGHFVHPTIFSGLRHDDRIMQEEIFGPVVGFATAKDFDQAIEYANATDY 440
                                           ************************************************************************* PP

                             TIGR01237 439 gltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                           gltG+vi+++re+ie+a+ +f vGnlyfnr +t aivg+qpfGGfkmsGtdskaGGpdyl+ ++q kt +e+
  NCBI__GCF_000330705.1:WP_017547991.1 441 GLTGAVITQNREHIEQARRDFMVGNLYFNRGCTAAIVGYQPFGGFKMSGTDSKAGGPDYLTLHMQGKTSSEQ 512
                                           ********************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (513 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.52
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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 2024 update 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