Alignments for a candidate for putA in Pontibacillus litoralis JSM 072002

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Pontibacillus litoralis JSM 072002

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_036835911.1 N784_RS14095 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000775615.1:WP_036835911.1
          Length = 515

 Score =  780 bits (2013), Expect = 0.0
 Identities = 381/514 (74%), Positives = 439/514 (85%)

Query: 1   MTTPYKHEPFTNFQDQNNVEAFKKALATVSEYLGKDYPLVINGERVETEAKIVSINPADK 60
           M TPYKHEPFT+F  + N +A++  L  V  YL ++Y L++NGER++T+ KIVS NPA  
Sbjct: 1   MYTPYKHEPFTDFSIEENKKAYEAGLEKVKSYLNQEYDLIVNGERIKTDDKIVSTNPAKT 60

Query: 61  EEVVGRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLV 120
           +EVVG VSKA+QE AEQA+QAA+ AFE+WR  S E RA +LFRAAAK+RRRKHEFSALL 
Sbjct: 61  DEVVGTVSKATQEIAEQAMQAASDAFEDWRKWSAEARAGILFRAAAKIRRRKHEFSALLS 120

Query: 121 KEAGKPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPP 180
            E GKPW EADADTAEAIDF+EYYARQ IE+ KGK V SREGE N YVYTP GV VVIPP
Sbjct: 121 YEVGKPWKEADADTAEAIDFLEYYARQAIEVDKGKHVESREGEMNCYVYTPCGVAVVIPP 180

Query: 181 WNFLFAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAE 240
           WN   AIMAGTTVAP+VTGNTVV+KPAS +PV AAKFVEVLEESGLPKGV+NFVPGSG E
Sbjct: 181 WNLALAIMAGTTVAPLVTGNTVVMKPASNSPVTAAKFVEVLEESGLPKGVLNFVPGSGKE 240

Query: 241 VGDYLVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDAD 300
           VGDYLVDHPKT+LI+FTGSR+VG RI ERAAK+QPGQ HLKRVIAEMGGKDTVVVD+ AD
Sbjct: 241 VGDYLVDHPKTALISFTGSRDVGVRIMERAAKLQPGQNHLKRVIAEMGGKDTVVVDKSAD 300

Query: 301 IELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMG 360
           IE A  +I  SAFGF+GQKCS+GSRAVVHE +YD+VL+RV ++T+         +++YMG
Sbjct: 301 IETAVNAIVVSAFGFSGQKCSSGSRAVVHEDIYDEVLDRVAKLTKELTVGNATESNIYMG 360

Query: 361 PVIDQGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGP 420
           PV+DQ ++DKIMSY+EIGK+EGRLV GGTGDDS GYFI+PTIFADL P +R+ QEEIFGP
Sbjct: 361 PVVDQAAFDKIMSYMEIGKEEGRLVVGGTGDDSTGYFIQPTIFADLAPTSRMQQEEIFGP 420

Query: 421 VVAFCKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVG 480
           VV F KV DFDEA+EVANNTEYGLTGAVI+ +R++IE+A ++FHVGNLYFNRNCTGAIVG
Sbjct: 421 VVCFTKVKDFDEAIEVANNTEYGLTGAVISEDRQNIEKAARDFHVGNLYFNRNCTGAIVG 480

Query: 481 YHPFGGFKMSGTDSKAGGPDYLALHMQAKTISEM 514
           Y PFGGFKMSGTDSKAGGPDYLALHMQAKTISEM
Sbjct: 481 YQPFGGFKMSGTDSKAGGPDYLALHMQAKTISEM 514


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: 905
Number of extensions: 26
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: 515
Length adjustment: 35
Effective length of query: 480
Effective length of database: 480
Effective search space:   230400
Effective search space used:   230400
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_036835911.1 N784_RS14095 (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.2446601.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-260  850.2   5.9   3.3e-260  850.1   5.9    1.0  1  NCBI__GCF_000775615.1:WP_036835911.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000775615.1:WP_036835911.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  850.1   5.9  3.3e-260  3.3e-260       1     510 [.       5     514 ..       5     515 .] 1.00

  Alignments for each domain:
  == domain 1  score: 850.1 bits;  conditional E-value: 3.3e-260
                             TIGR01237   1 yknepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasvedaeq 73 
                                           yk+epftdf+ ee+++a+++ l kvk +l ++y l++nGe+++t++ki+s npa+++evvG+v+ka++e aeq
  NCBI__GCF_000775615.1:WP_036835911.1   5 YKHEPFTDFSIEENKKAYEAGLEKVKSYLNQEYDLIVNGERIKTDDKIVSTNPAKTDEVVGTVSKATQEIAEQ 77 
                                           9************************************************************************ PP

                             TIGR01237  74 alqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfleyyaremik 146
                                           a+qaa  afe+w+k++ e+ra+il++aaa+++rr+he+sall+ evGk+++eada++aeaidfleyyar++i+
  NCBI__GCF_000775615.1:WP_036835911.1  78 AMQAASDAFEDWRKWSAEARAGILFRAAAKIRRRKHEFSALLSYEVGKPWKEADADTAEAIDFLEYYARQAIE 150
                                           ************************************************************************* PP

                             TIGR01237 147 lakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaatviaaklveilee 219
                                           ++k+k+v s+eGe n y+y+p Gvavvi+pwn+ lai++G+tvap+vtGn+vv+kpa++++v aak+ve+lee
  NCBI__GCF_000775615.1:WP_036835911.1 151 VDKGKHVESREGEMNCYVYTPCGVAVVIPPWNLALAIMAGTTVAPLVTGNTVVMKPASNSPVTAAKFVEVLEE 223
                                           ************************************************************************* PP

                             TIGR01237 220 aGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhlkrviaelGGkdavivd 292
                                           +GlpkGvl+fvpG+G+evG+ylvdhpkt li+ftGsr+vG+ri+e+aak+qpGq+hlkrviae+GGkd+v+vd
  NCBI__GCF_000775615.1:WP_036835911.1 224 SGLPKGVLNFVPGSGKEVGDYLVDHPKTALISFTGSRDVGVRIMERAAKLQPGQNHLKRVIAEMGGKDTVVVD 296
                                           ************************************************************************* PP

                             TIGR01237 293 esadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkvgktdeadvqvgpvidqksfd 365
                                           +sadie+av+a+v safGf+Gqkcs++sr+vv+e++ydev++r+ + tk l+vg++ e+++++gpv+dq +fd
  NCBI__GCF_000775615.1:WP_036835911.1 297 KSADIETAVNAIVVSAFGFSGQKCSSGSRAVVHEDIYDEVLDRVAKLTKELTVGNATESNIYMGPVVDQAAFD 369
                                           ************************************************************************* PP

                             TIGR01237 366 kikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeifGpvvavlrakdfdealeianstey 438
                                           ki++y+e+gk+eg+lv+gg++dds Gyfi+ptif+d+ + +r+ qeeifGpvv++ ++kdfdea+e+an+tey
  NCBI__GCF_000775615.1:WP_036835911.1 370 KIMSYMEIGKEEGRLVVGGTGDDSTGYFIQPTIFADLAPTSRMQQEEIFGPVVCFTKVKDFDEAIEVANNTEY 442
                                           ************************************************************************* PP

                             TIGR01237 439 gltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGfkmsGtdskaGGpdylaqflqaktvter 510
                                           gltG+vis+ r++ie+a+ +f+vGnlyfnr++tGaivg+qpfGGfkmsGtdskaGGpdyla ++qakt++e+
  NCBI__GCF_000775615.1:WP_036835911.1 443 GLTGAVISEDRQNIEKAARDFHVGNLYFNRNCTGAIVGYQPFGGFKMSGTDSKAGGPDYLALHMQAKTISEM 514
                                           ***********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (515 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 15.16
//
[ok]

This GapMind analysis is from Sep 24 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 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