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_013074879.1 BTUS_RS04205 L-glutamate gamma-semialdehyde dehydrogenase

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000092905.1:WP_013074879.1
          Length = 513

 Score =  562 bits (1448), Expect = e-164
 Identities = 276/510 (54%), Positives = 359/510 (70%), Gaps = 1/510 (0%)

Query: 5   YKHEPFTNFQDQNNVEAFKKALATVSEYLGKDYPLVINGERVETEAKIVSINPADKEEVV 64
           +++EP +NF D    +  K+ALA V   LG+ YPLV+ G RV+T ++I S+NPA  ++V+
Sbjct: 4   FRNEPLSNFHDPAVRDRMKEALAQVEGMLGQYYPLVLGGRRVDTASRITSVNPAQIDQVI 63

Query: 65  GRVSKASQEHAEQAIQAAAKAFEEWRYTSPEERAAVLFRAAAKVRRRKHEFSALLVKEAG 124
           G V+     H ++A++A  KAF EW     E RA  LF+AAA +RRRK EF+A +V E G
Sbjct: 64  GEVAAGDASHVDKAVEAGWKAFPEWGRLPAEARAGYLFQAAAALRRRKFEFAAWMVYEVG 123

Query: 125 KPWNEADADTAEAIDFMEYYARQMIELAKGKPVNSREGEKNQYVYTPTGVTVVIPPWNFL 184
           K W EADAD AEAIDF+EYY R+ I L KG  +    GE N+  Y P GV  +I PWNF 
Sbjct: 124 KNWAEADADVAEAIDFLEYYGREAIRLGKGASLVPHPGEDNRMTYIPLGVGAIIAPWNFP 183

Query: 185 FAIMAGTTVAPIVTGNTVVLKPASATPVIAAKFVEVLEESGLPKGVVNFVPGSGAEVGDY 244
            AI+ G + A +VTGN V++KP+S  PV+AAK+VE+LEE G+P GVV ++PG G  VGD 
Sbjct: 184 VAILVGMSSAALVTGNPVIIKPSSQAPVVAAKWVELLEEIGVPAGVVQYLPGPGGAVGDA 243

Query: 245 LVDHPKTSLITFTGSREVGTRIFERAAKVQPGQQHLKRVIAEMGGKDTVVVDEDADIELA 304
           LVDHP    + FTGS+EVG RI +RAA   PG + +KRV+AEMGGKD ++VDE AD+  A
Sbjct: 244 LVDHPGVRFVNFTGSKEVGLRIVQRAATPAPGCRWIKRVVAEMGGKDGIIVDETADLGAA 303

Query: 305 AQSIFTSAFGFAGQKCSAGSRAVVHEKVYDQVLERVIEITESKVTAKPDSADVYMGPVID 364
            Q I TSAFGF GQKCSAGSRA+V   VYD+V+ER+ E  +     KP + +  MGPVID
Sbjct: 304 VQGILTSAFGFQGQKCSAGSRAIVVRSVYDEVVERLREGVKQWTVGKP-ADNAPMGPVID 362

Query: 365 QGSYDKIMSYIEIGKQEGRLVSGGTGDDSKGYFIKPTIFADLDPKARLMQEEIFGPVVAF 424
           + +Y KI+ Y+EIG++EGRLV+GG   +  GY+++PTIFAD+ P+AR+ QEEIFGPV+A 
Sbjct: 363 ESAYRKILHYMEIGREEGRLVAGGRPAEGPGYYLQPTIFADVHPRARIAQEEIFGPVLAV 422

Query: 425 CKVSDFDEALEVANNTEYGLTGAVITNNRKHIERAKQEFHVGNLYFNRNCTGAIVGYHPF 484
                F+EA+E  N+TEYGLTG++ T  R  +E  ++    GNLY NR CTGA+VG HPF
Sbjct: 423 IPADSFEEAVETFNDTEYGLTGSLYTRRRDRVEYVREHMFCGNLYINRKCTGALVGVHPF 482

Query: 485 GGFKMSGTDSKAGGPDYLALHMQAKTISEM 514
           GGF MSGTDSKAGGPDYL L  QAK +SE+
Sbjct: 483 GGFNMSGTDSKAGGPDYLLLFTQAKVVSEV 512


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: 809
Number of extensions: 34
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_013074879.1 BTUS_RS04205 (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.4413.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-220  717.5   0.0   5.6e-220  717.3   0.0    1.0  1  lcl|NCBI__GCF_000092905.1:WP_013074879.1  BTUS_RS04205 L-glutamate gamma-s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092905.1:WP_013074879.1  BTUS_RS04205 L-glutamate gamma-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.3   0.0  5.6e-220  5.6e-220       1     510 [.       4     512 ..       4     513 .] 1.00

  Alignments for each domain:
  == domain 1  score: 717.3 bits;  conditional E-value: 5.6e-220
                                 TIGR01237   1 yknepftdfadeelvqafkkalakvkellGkdyplvinGeeveteakidsinpadksevvGkvakasve 69 
                                               ++nep ++f+d   ++ +k+ala+v+ +lG+ yplv+ G++v+t+++i+s+npa+ ++v+G+va     
  lcl|NCBI__GCF_000092905.1:WP_013074879.1   4 FRNEPLSNFHDPAVRDRMKEALAQVEGMLGQYYPLVLGGRRVDTASRITSVNPAQIDQVIGEVAAGDAS 72 
                                               689****************************************************************** PP

                                 TIGR01237  70 daeqalqaakkafeewkktdveeraaillkaaailkrrrhelsallvlevGkiyaeadaevaeaidfle 138
                                               + ++a++a +kaf+ew + + e+ra+ l++aaa l+rr++e++a++v evGk++aeada+vaeaidfle
  lcl|NCBI__GCF_000092905.1:WP_013074879.1  73 HVDKAVEAGWKAFPEWGRLPAEARAGYLFQAAAALRRRKFEFAAWMVYEVGKNWAEADADVAEAIDFLE 141
                                               ********************************************************************* PP

                                 TIGR01237 139 yyaremiklakskevlsieGeknrylyiplGvavvispwnfplailvGmtvapivtGncvvlkpaeaat 207
                                               yy re+i+l k+ +    +Ge+nr+ yiplGv+ +i+pwnfp+ailvGm+ a++vtGn v++kp+++a+
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 142 YYGREAIRLGKGASLVPHPGEDNRMTYIPLGVGAIIAPWNFPVAILVGMSSAALVTGNPVIIKPSSQAP 210
                                               ********************************************************************* PP

                                 TIGR01237 208 viaaklveileeaGlpkGvlqfvpGkGsevGeylvdhpktrlitftGsrevGlriyedaakvqpGqkhl 276
                                               v+aak ve+lee G+p+Gv+q++pG G  vG+ lvdhp +r++ ftGs+evGlri ++aa   pG +++
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 211 VVAAKWVELLEEIGVPAGVVQYLPGPGGAVGDALVDHPGVRFVNFTGSKEVGLRIVQRAATPAPGCRWI 279
                                               ********************************************************************* PP

                                 TIGR01237 277 krviaelGGkdavivdesadieqavaaavtsafGfaGqkcsaasrvvvlekvydevverfveatkslkv 345
                                               krv+ae+GGkd++ivde+ad+  av++++tsafGf+Gqkcsa+sr++v+ +vydevver+ e  k  +v
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 280 KRVVAEMGGKDGIIVDETADLGAAVQGILTSAFGFQGQKCSAGSRAIVVRSVYDEVVERLREGVKQWTV 348
                                               ********************************************************************* PP

                                 TIGR01237 346 gktdeadvqvgpvidqksfdkikeyielgkaegklvlggedddskGyfikptifkdvdrkarlaqeeif 414
                                               gk+ + ++ +gpvid+ ++ ki +y+e+g++eg+lv gg  ++  Gy+++ptif+dv ++ar+aqeeif
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 349 GKPAD-NAPMGPVIDESAYRKILHYMEIGREEGRLVAGGRPAEGPGYYLQPTIFADVHPRARIAQEEIF 416
                                               *****.9************************************************************** PP

                                 TIGR01237 415 GpvvavlrakdfdealeiansteygltGgvisnsrerierakaefevGnlyfnrkitGaivgvqpfGGf 483
                                               Gpv+av+ a  f+ea+e  n+teygltG+++++ r+r+e  ++ +  Gnly+nrk+tGa+vgv+pfGGf
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 417 GPVLAVIPADSFEEAVETFNDTEYGLTGSLYTRRRDRVEYVREHMFCGNLYINRKCTGALVGVHPFGGF 485
                                               ********************************************************************* PP

                                 TIGR01237 484 kmsGtdskaGGpdylaqflqaktvter 510
                                               +msGtdskaGGpdyl+ f qak v+e 
  lcl|NCBI__GCF_000092905.1:WP_013074879.1 486 NMSGTDSKAGGPDYLLLFTQAKVVSEV 512
                                               *************************96 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.87
//
[ok]

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

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Protein sequences (fasta format)
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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