Alignments for a candidate for putA in Kyrpidia tusciae DSM 2912

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Kyrpidia tusciae DSM 2912

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_041303623.1 BTUS_RS02575 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000092905.1:WP_041303623.1
          Length = 517

 Score =  587 bits (1513), Expect = e-172
 Identities = 290/511 (56%), Positives = 371/511 (72%)

Query: 5   YKHEPFTNFQDQNNVEAFKKALATVSEYLGKDYPLVINGERVETEAKIVSINPADKEEVV 64
           +++EP TNFQD     A K AL  V    G++YP+ I+G    +   I S +P+  +E+V
Sbjct: 7   FRNEPLTNFQDPAFHRAMKDALEDVRRGFGREYPMRIDGRDRFSGHWIRSADPSRPKELV 66

Query: 65  GRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAG 124
           G+V+ A++E A  A++ A  AF+ W     E RA  LF+AAA +RRRK   +AL+  E G
Sbjct: 67  GQVAAATREDAMDAVEGAWSAFKSWSRVPAEARARCLFKAAAIMRRRKFHLAALMCFEVG 126

Query: 125 KPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFL 184
           K W+EADAD AEAIDF+E+Y R+MI LA+  P+   +GE N+  Y P GV VVIPPWNF 
Sbjct: 127 KTWSEADADVAEAIDFLEFYGREMIRLARPHPLTRIQGEDNEVTYEPLGVGVVIPPWNFP 186

Query: 185 FAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDY 244
            AI+ G TV+ +V GN VVLKPASA+PVIAA+F +++EE+G+P GV+ F+PGSG E+GD 
Sbjct: 187 LAILTGMTVSSVVAGNAVVLKPASASPVIAAEFAKIMEEAGIPPGVIQFLPGSGGEIGDV 246

Query: 245 LVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELA 304
           LV HP+   +TFTGSR+VG  I+E AAKVQPGQ+ LKRVIAEMGGKD ++VD DAD++ A
Sbjct: 247 LVSHPQVRFVTFTGSRDVGVHIYELAAKVQPGQKWLKRVIAEMGGKDAIIVDSDADLDDA 306

Query: 305 AQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVID 364
           A  I TSAFGFAGQKCSA SR +  + VY+ +LERV  +TE    A  D  +   GPV+D
Sbjct: 307 AAGIVTSAFGFAGQKCSACSRVIALDDVYEPILERVRALTERLKVAPADLEEASYGPVVD 366

Query: 365 QGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAF 424
           + +YDK++ YIEIG+ EG+LV+GG   +  GYFIKPTIF D+ P+AR+ QEEIFGPV+AF
Sbjct: 367 RAAYDKVLQYIEIGQTEGQLVTGGGPAEGDGYFIKPTIFRDVPPEARIAQEEIFGPVLAF 426

Query: 425 CKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPF 484
            K  DFDEAL +AN T+YGLTG V + NR H+E+A++EF VGNLYFNR  TGA+VG HPF
Sbjct: 427 LKAKDFDEALRIANGTQYGLTGGVYSRNRAHLEQARREFEVGNLYFNRKITGALVGAHPF 486

Query: 485 GGFKMSGTDSKAGGPDYLALHMQAKTISEMF 515
           GGF MSGTDSKAGG DYL L  QAK +SE F
Sbjct: 487 GGFHMSGTDSKAGGQDYLLLLTQAKVVSERF 517


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: 780
Number of extensions: 22
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: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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_041303623.1 BTUS_RS02575 (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.16329.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-233  760.0   0.0   7.3e-233  759.8   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_041303623.1  BTUS_RS02575 L-glutamate gamma-s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_041303623.1  BTUS_RS02575 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  759.8   0.0  7.3e-233  7.3e-233       1     511 []       7     517 .]       7     517 .] 1.00

  Alignments for each domain:
  == domain 1  score: 759.8 bits;  conditional E-value: 7.3e-233
                                 TIGR01237   1 yknepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasve 69 
                                               ++nep t+f+d  + +a+k+al  v++ +G++yp+ i+G+   +   i s +p++++e vG+va a+ e
  lcl|NCBI__GCF_000092905.1:WP_041303623.1   7 FRNEPLTNFQDPAFHRAMKDALEDVRRGFGREYPMRIDGRDRFSGHWIRSADPSRPKELVGQVAAATRE 75 
                                               689****************************************************************** PP

                                 TIGR01237  70 daeqalqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfle 138
                                               da +a+++a+ af++w +++ e+ra+ l+kaaai++rr++ l+al++ evGk+++eada+vaeaidfle
  lcl|NCBI__GCF_000092905.1:WP_041303623.1  76 DAMDAVEGAWSAFKSWSRVPAEARARCLFKAAAIMRRRKFHLAALMCFEVGKTWSEADADVAEAIDFLE 144
                                               ********************************************************************* PP

                                 TIGR01237 139 yyaremiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaat 207
                                               +y remi+la+ ++ + i+Ge+n+  y plGv+vvi+pwnfplail Gmtv+++v+Gn+vvlkpa+a++
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 145 FYGREMIRLARPHPLTRIQGEDNEVTYEPLGVGVVIPPWNFPLAILTGMTVSSVVAGNAVVLKPASASP 213
                                               ********************************************************************* PP

                                 TIGR01237 208 viaaklveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhl 276
                                               viaa +++i+eeaG+p+Gv+qf+pG+G e+G+ lv+hp++r++tftGsr+vG++iye aakvqpGqk+l
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 214 VIAAEFAKIMEEAGIPPGVIQFLPGSGGEIGDVLVSHPQVRFVTFTGSRDVGVHIYELAAKVQPGQKWL 282
                                               ********************************************************************* PP

                                 TIGR01237 277 krviaelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkv 345
                                               krviae+GGkda+ivd +ad+++a+a++vtsafGfaGqkcsa+srv+ l++vy+ ++er+   t+ lkv
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 283 KRVIAEMGGKDAIIVDSDADLDDAAAGIVTSAFGFAGQKCSACSRVIALDDVYEPILERVRALTERLKV 351
                                               ********************************************************************* PP

                                 TIGR01237 346 gktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeif 414
                                               +++d  ++  gpv+d+ ++dk+ +yie+g++eg+lv gg  ++ +Gyfikptif+dv ++ar+aqeeif
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 352 APADLEEASYGPVVDRAAYDKVLQYIEIGQTEGQLVTGGGPAEGDGYFIKPTIFRDVPPEARIAQEEIF 420
                                               ********************************************************************* PP

                                 TIGR01237 415 GpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGf 483
                                               Gpv+a+l+akdfdeal ian+t+ygltGgv+s++r ++e+a+ efevGnlyfnrkitGa+vg +pfGGf
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 421 GPVLAFLKAKDFDEALRIANGTQYGLTGGVYSRNRAHLEQARREFEVGNLYFNRKITGALVGAHPFGGF 489
                                               ********************************************************************* PP

                                 TIGR01237 484 kmsGtdskaGGpdylaqflqaktvteri 511
                                               +msGtdskaGG dyl+   qak v+er+
  lcl|NCBI__GCF_000092905.1:WP_041303623.1 490 HMSGTDSKAGGQDYLLLLTQAKVVSERF 517
                                               **************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (511 nodes)
Target sequences:                          1  (517 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 12.24
//
[ok]

This GapMind analysis is from Sep 24 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:

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