Alignments for a candidate for putA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Echinicola vietnamensis KMM 6221, DSM 17526

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1

Query= BRENDA::P30038
         (563 letters)



>FitnessBrowser__Cola:Echvi_1300
          Length = 543

 Score =  513 bits (1321), Expect = e-150
 Identities = 258/530 (48%), Positives = 351/530 (66%), Gaps = 3/530 (0%)

Query: 34  NEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAK 93
           NEPV  +  G+P R  LQ AL++ + +   +P  +G EEV T +      P +H H +  
Sbjct: 13  NEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGNKIPLSPPHDHQHLLGH 72

Query: 94  FCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGK 153
           F   DKS + +AI AAL A++ W+      RA IFLKAAD+++GP R ++ A TM+GQ K
Sbjct: 73  FHEGDKSHVEQAINAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSK 132

Query: 154 TVIQAEIDAAAELIDFFRFNAKYAVELEGQQP-ISVPPSTNSTVYRGLEGFVAAISPFNF 212
              QAEID+A E++DF RFN KY  E+  QQP IS     N    R LEGFV A++PFNF
Sbjct: 133 NAFQAEIDSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNF 192

Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272
           TAI GNL  APA+MGN V+WKP+ T +  +  + ++ REAG+P  +I  V  DGP  G+ 
Sbjct: 193 TAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAGEV 252

Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332
           +       GI+FTGS   F+ +WK +  N++++ ++PR+ GE GGK+F   H+SAD + +
Sbjct: 253 IFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAKQL 312

Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392
            +G +R AFE+ GQKCSA SR Y+P +LW  +K  + E+ + IK+G P EDF  F +AVI
Sbjct: 313 ATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGP-EDFSNFINAVI 371

Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPV 452
           D KSF +I K+++ A+S   L ++AGG  D S GYFVEP ++ +KDP    M EEIFGPV
Sbjct: 372 DEKSFDKIAKYIDTAKSD-GLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPV 430

Query: 453 LSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTG 512
           L++YVY +D ++E L+LVD T+ YGLTGA+FS D+   Q AT+ LRNAAGNFYINDK TG
Sbjct: 431 LTIYVYQEDHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTG 490

Query: 513 SIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562
           ++VGQQPFGGAR SGTNDK G    +LRW SP+ IKET     D+ Y ++
Sbjct: 491 AVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIKETFVTPTDYRYPFL 540


Lambda     K      H
   0.319    0.135    0.411 

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: 870
Number of extensions: 37
Number of successful extensions: 4
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: 563
Length of database: 543
Length adjustment: 36
Effective length of query: 527
Effective length of database: 507
Effective search space:   267189
Effective search space used:   267189
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate Echvi_1300 Echvi_1300 (delta-1-pyrroline-5-carboxylate dehydrogenase, group 1)
to HMM TIGR01236 (pruA: 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.23446.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.6e-246  804.2   0.2     3e-246  804.1   0.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1300  Echvi_1300 delta-1-pyrroline-5-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1300  Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  804.1   0.2    3e-246    3e-246       1     531 [.      12     539 ..      12     541 .. 0.99

  Alignments for each domain:
  == domain 1  score: 804.1 bits;  conditional E-value: 3e-246
                            TIGR01236   1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                          knePv +++pg+++r +l+++l+e++sk +++P+ ig +ev + n +i    P+dhq+ l+++++ ++++v++a
  lcl|FitnessBrowser__Cola:Echvi_1300  12 KNEPVFDYAPGTPARAKLQAALQEARSKEVDVPMYIGSEEVRTGN-KIPLSPPHDHQHLLGHFHEGDKSHVEQA 84 
                                          6***************************************66655.7*************************** PP

                            TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyare 148
                                          ++aal ak+ W+++++++raaiflkaadl++g+yr++++aatmlgqsk+ +qaeid+++e++df+rfnvky +e
  lcl|FitnessBrowser__Cola:Echvi_1300  85 INAALGAKEAWETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSKNAFQAEIDSACEIVDFLRFNVKYMTE 158
                                          ************************************************************************** PP

                            TIGR01236 149 lleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkileea 222
                                          +++qqP +s++g++n+ e rpleGfv+a++Pfnftaia+nl++aPa+mGn+vvWkP+ t+++++ llm++++ea
  lcl|FitnessBrowser__Cola:Echvi_1300 159 IYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNFTAIAGNLPTAPAMMGNTVVWKPAYTQIYTANLLMQVFREA 232
                                          ************************************************************************** PP

                            TIGR01236 223 GlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlvhps 296
                                          G+P gvin+v +dg + ++v+  ++++a++hftGstavf+++wk++ +n++ky+++PrivGetGGkdfv++h+s
  lcl|FitnessBrowser__Cola:Echvi_1300 233 GVPDGVINLVYVDGPAAGEVIFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKS 306
                                          ************************************************************************** PP

                            TIGR01236 297 adveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksfakiv 370
                                          ad ++++++++rgafe+qGqkcsaasr+y+p  lw+++k+ + ++l+++k+g ++d+s+f+ avideksf+ki 
  lcl|FitnessBrowser__Cola:Echvi_1300 307 ADAKQLATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGPEDFSNFINAVIDEKSFDKIA 380
                                          ************************************************************************** PP

                            TIGR01236 371 kviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilevvdsts 444
                                          k+i++ak+d   le++aGG+yd+skGyfvePtv+++kdP   +m eeifGPvlt+yvy++d+++e le+vd+ts
  lcl|FitnessBrowser__Cola:Echvi_1300 381 KYIDTAKSDG--LEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPVLTIYVYQEDHFEEALELVDQTS 452
                                          ********88..************************************************************** PP

                            TIGR01236 445 kyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfvsarsik 518
                                           y+ltGa+f++dr a + a++klr+aaGnfyindk+tGavvgqqpfGGar sGtndkaGa+ ++lr+vs+r+ik
  lcl|FitnessBrowser__Cola:Echvi_1300 453 PYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTGAVVGQQPFGGARKSGTNDKAGAMINMLRWVSPRTIK 526
                                          ************************************************************************** PP

                            TIGR01236 519 etfkeltdfkypy 531
                                          etf+++td++yp+
  lcl|FitnessBrowser__Cola:Echvi_1300 527 ETFVTPTDYRYPF 539
                                          ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (543 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 6.39
//
[ok]

This GapMind analysis is from Sep 17 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 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