GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Galbibacter marinus ck-I2-15

Align delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized)
to candidate WP_008991251.1 I215_RS06920 L-glutamate gamma-semialdehyde dehydrogenase

Query= CharProtDB::CH_122352
         (572 letters)



>NCBI__GCF_000300875.1:WP_008991251.1
          Length = 543

 Score =  519 bits (1336), Expect = e-151
 Identities = 276/540 (51%), Positives = 353/540 (65%), Gaps = 8/540 (1%)

Query: 30  YKVPRIDNEPNKHYAAGSPDRKALQEALARTQRNAPLSVPLVIAGKEVKSSSSLTQSNPA 89
           + VP+  NEP K YA GSP+R A+ E   +   N+ + +P+ I  +EV++ ++   S P 
Sbjct: 6   FHVPKAVNEPVKSYAPGSPERAAVLEQYDQ-YFNSTVDIPMYIGSEEVRTGNTQPLSPPH 64

Query: 90  SHGP-VATYSNATAKDVQAAIESALEARKSWASTPFADRASVFLKAADLISTKYRYDVMA 148
            H   V  Y  A    V  AI + LEAR  WA+  +  RA+VFLKAA+LI+  YR  + A
Sbjct: 65  DHQHIVGKYHLADKSLVSKAIANNLEARGKWAALSWEQRAAVFLKAAELIAGPYRAKINA 124

Query: 149 LTMHGQGKNAWQAEIDSAAELCDFFRFGVKYAEDLYAQQPVHHAPGVWNRVEYRPLEGFV 208
            TM  Q KN  QAEIDSA EL DF  F +++  ++Y  QP   + G+WNRVEYRPLEGFV
Sbjct: 125 ATMIAQSKNIHQAEIDSACELIDFLNFNIEFMSNIYQDQPKSES-GIWNRVEYRPLEGFV 183

Query: 209 YAISPFNFTAIGGNLAGAPALMGNVVVWKPSPSAIASNWLVHQILLEAGLPKNVIQFVPG 268
           YA++PFNFTAI GNL  + A+MGNVV+WKPS S I S  ++  I  EAGLP  VI  V G
Sbjct: 184 YAVTPFNFTAIAGNLPASAAMMGNVVLWKPSDSQIYSAKVIVDIFKEAGLPDGVINVVYG 243

Query: 269 EAEEVTKTVLDHPDFAALHFTGSTNVFRNLYGQISTRVAAGKYRSYPRIVGETGGKNFHL 328
           + + +T TVL  PDFA +HFTGST+VF++++  I   +    Y+SYPRIVGETGGK+F +
Sbjct: 244 DPQMITDTVLSSPDFAGIHFTGSTSVFKSIWKNIGNNIDI--YKSYPRIVGETGGKDFII 301

Query: 329 IHKSADIRNAAVQTVRGAFEYQGQKCSATSRVYVASSIADSFLEQVASEAKSLKVGPPSD 388
            H S++ +  A    RGAFE+QGQKCSA SRVY+  SIA   L+ V  + +S K+G P+ 
Sbjct: 302 AHPSSNPKQVATAISRGAFEFQGQKCSAASRVYLPESIASQVLDFVKQDVESFKIGAPNQ 361

Query: 389 FTNFCGPVIHEASFTKLAKVIDEAKNDPELELLAGGSYDSSKGWYIQPTVYRTTNPDHPL 448
             NF   VIHE SF KLA  ID+AK D + E+  GG+YD SKG++I PTV  TT+P +  
Sbjct: 362 MENFITAVIHEGSFDKLASYIDQAKEDADAEIFVGGTYDKSKGYFIHPTVIVTTDPKYKT 421

Query: 449 LTRELFGPILVVYAYPDATEADFARIAQKIDATGEYGLTGSVFAQDREALAVANDVLRNA 508
           +T ELFGP++ VY Y D     +A     +D T EYGLTG+VF+ DR  +  A   L+N+
Sbjct: 422 MTTELFGPVVTVYVYKD---DQWAETLNLVDTTSEYGLTGAVFSNDRYTIEEATTALQNS 478

Query: 509 AGNFYINCKSTGAVVGQQPFGGARASGTNDKAGSGNLLSRFVSLRSIKEEFVPTYKVAYP 568
           AGNFYIN K TGAVVGQQPFGGARASGTNDKAGS   L R+VS R IKE FV      YP
Sbjct: 479 AGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRWVSPRLIKETFVTPVDYRYP 538


Lambda     K      H
   0.316    0.130    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: 914
Number of extensions: 41
Number of successful extensions: 6
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: 572
Length of database: 543
Length adjustment: 36
Effective length of query: 536
Effective length of database: 507
Effective search space:   271752
Effective search space used:   271752
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: 53 (25.0 bits)

Align candidate WP_008991251.1 I215_RS06920 (L-glutamate gamma-semialdehyde dehydrogenase)
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.662525.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-235  767.3   1.6   4.7e-235  767.1   1.6    1.0  1  NCBI__GCF_000300875.1:WP_008991251.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000300875.1:WP_008991251.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  767.1   1.6  4.7e-235  4.7e-235       2     531 ..      13     539 ..      12     541 .. 0.99

  Alignments for each domain:
  == domain 1  score: 767.1 bits;  conditional E-value: 4.7e-235
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           nePvk+++pgs+er ++ ++  +  +++++iP+ ig +ev  +++++    P+dhq+ ++k + a++++v+ka
  NCBI__GCF_000300875.1:WP_008991251.1  13 NEPVKSYAPGSPERAAVLEQYDQYFNSTVDIPMYIGSEEVR-TGNTQPLSPPHDHQHIVGKYHLADKSLVSKA 84 
                                           9***************9999******************955.5558*************************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           + + l+a+ +W++l +++raa+flkaa+l++g+yr++i+aatm++qsk+++qaeid+++elidf+ fn+++ +
  NCBI__GCF_000300875.1:WP_008991251.1  85 IANNLEARGKWAALSWEQRAAVFLKAAELIAGPYRAKINAATMIAQSKNIHQAEIDSACELIDFLNFNIEFMS 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           ++++ qP +s +g +n+veyrpleGfv+a++Pfnftaia+nl+++ a+mGnvv+WkPs+ +++s+ +++ i++
  NCBI__GCF_000300875.1:WP_008991251.1 158 NIYQDQP-KSESGIWNRVEYRPLEGFVYAVTPFNFTAIAGNLPASAAMMGNVVLWKPSDSQIYSAKVIVDIFK 229
                                           *******.79*************************************************************** PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaGlP gvin+v +d+ +++d+vl+++d+a++hftGst+vfk++wk++ +n+d y+++PrivGetGGkdf+++
  NCBI__GCF_000300875.1:WP_008991251.1 230 EAGLPDGVINVVYGDPQMITDTVLSSPDFAGIHFTGSTSVFKSIWKNIGNNIDIYKSYPRIVGETGGKDFIIA 302
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366
                                           hps++ ++v++a+ rgafe+qGqkcsaasr+y+p+s+  ++ + ++++ ++ k+g ++++++f++avi+e sf
  NCBI__GCF_000300875.1:WP_008991251.1 303 HPSSNPKQVATAISRGAFEFQGQKCSAASRVYLPESIASQVLDFVKQDVESFKIGAPNQMENFITAVIHEGSF 375
                                           ************************************************************************* PP

                             TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439
                                           +k+ ++i++ak+d+ + ei +GG yd+skGyf++Ptv+ + dPk k+m++e+fGPv+tvyvy+dd++ e+l++
  NCBI__GCF_000300875.1:WP_008991251.1 376 DKLASYIDQAKEDA-DAEIFVGGTYDKSKGYFIHPTVIVTTDPKYKTMTTELFGPVVTVYVYKDDQWAETLNL 447
                                           ************99.99******************************************************** PP

                             TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512
                                           vd+ts+y+ltGavf++dr +ieea+ +l+++aGnfyindk+tGavvgqqpfGGar+sGtndkaG++++llr+v
  NCBI__GCF_000300875.1:WP_008991251.1 448 VDTTSEYGLTGAVFSNDRYTIEEATTALQNSAGNFYINDKPTGAVVGQQPFGGARASGTNDKAGSAQNLLRWV 520
                                           ************************************************************************* PP

                             TIGR01236 513 sarsiketfkeltdfkypy 531
                                           s+r iketf+++ d++yp+
  NCBI__GCF_000300875.1:WP_008991251.1 521 SPRLIKETFVTPVDYRYPF 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.00
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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