Alignments for a candidate for rocA in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Amycolatopsis halophila YIM 93223

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_034270111.1 AMYHA_RS09435 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::P30038
         (563 letters)



>NCBI__GCF_000504245.1:WP_034270111.1
          Length = 542

 Score =  499 bits (1284), Expect = e-145
 Identities = 256/531 (48%), Positives = 331/531 (62%), Gaps = 3/531 (0%)

Query: 34  NEPVLAFTQGSPERDALQKALKDLKGRM-EAIPCVVGDEEVWTSDVQYQVSPFNHGHKVA 92
           NEPV  +  G+ ER +LQ+ L DL     E    + G++ +   +    V P  HGH + 
Sbjct: 12  NEPVYTYAPGTAERQSLQRTLTDLSSTTHELTQTIAGEQRMAGGEPFRVVKPHEHGHTLG 71

Query: 93  KFCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQG 152
               A    +  A+ AA  A   W   P  +RA +FL+AAD+L+GP R  I A TM+GQ 
Sbjct: 72  NCAQATPGEVTDAVTAAKEAAPAWREMPFDERAAVFLRAADLLAGPYRDTINAATMLGQS 131

Query: 153 KTVIQAEIDAAAELIDFFRFNAKYAVELEGQQPISVPPSTNSTVYRGLEGFVAAISPFNF 212
           K++ QAEIDAA ELIDF RFN  YA  +  +QP SVP   N   YR LEGFV AI+PFNF
Sbjct: 132 KSIQQAEIDAACELIDFLRFNVHYARRIYAEQPNSVPGVWNRMEYRSLEGFVTAITPFNF 191

Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272
           TAI GNL  APALMGN V+WKP+ T  LA++   R+L  AGLPP +I  V  DG    + 
Sbjct: 192 TAIAGNLPTAPALMGNTVVWKPTPTQQLAAHFTMRVLEAAGLPPGVINMVTGDGKAVSEV 251

Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332
             +     G++FTGS  TFK LW+ + +NLDR+  +PR+ GE GGK+F   H SA  +++
Sbjct: 252 ALADPDFAGLHFTGSTATFKLLWRTIGENLDRYKHYPRIVGETGGKDFVIAHPSARTDTL 311

Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWP-QIKGRLLEEHSRIKVGDPAEDFGTFFSAV 391
           V+  +R AFEY GQKCSA SR Y+  SLW   ++ +L +    I  GD   D   F  AV
Sbjct: 312 VTALVRGAFEYQGQKCSAVSRAYIARSLWEGGVRDQLADVTKTISYGD-VSDLSHFGGAV 370

Query: 392 IDAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGP 451
           IDA++FA+ K  L+     P+L +L GG CDDSVGYFV+P I+ + DP   +  +E FGP
Sbjct: 371 IDARAFAKHKALLDSVDGDPALDVLVGGGCDDSVGYFVDPTILVASDPNHEVFSKEYFGP 430

Query: 452 VLSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKST 511
           + +VYVY DD Y E L+LVDS+  Y LTG VF+ D+D +Q+A + L  AAGNFY+NDK T
Sbjct: 431 ICAVYVYEDDDYAEALRLVDSSAPYALTGGVFADDRDAIQQAHRALGYAAGNFYVNDKPT 490

Query: 512 GSIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562
           GSIVGQQPFGGARASGTNDK G    + RW SP+ IKE      D +Y +M
Sbjct: 491 GSIVGQQPFGGARASGTNDKAGSMFNLQRWASPRSIKENFVAPTDHTYPHM 541


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: 871
Number of extensions: 34
Number of successful extensions: 3
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: 542
Length adjustment: 36
Effective length of query: 527
Effective length of database: 506
Effective search space:   266662
Effective search space used:   266662
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 WP_034270111.1 AMYHA_RS09435 (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.2878787.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-242  791.7   0.0   1.9e-242  791.5   0.0    1.0  1  NCBI__GCF_000504245.1:WP_034270111.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034270111.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  791.5   0.0  1.9e-242  1.9e-242       1     532 [.      11     541 ..      11     542 .] 0.99

  Alignments for each domain:
  == domain 1  score: 791.5 bits;  conditional E-value: 1.9e-242
                             TIGR01236   1 knePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkk 73 
                                           +nePv  ++pg+ er+ l+++l++l s++ e+   i+g++++  +e ++vv+P++h + l++  +at+ +v++
  NCBI__GCF_000504245.1:WP_034270111.1  11 RNEPVYTYAPGTAERQSLQRTLTDLSSTTHELTQTIAGEQRMAGGEPFRVVKPHEHGHTLGNCAQATPGEVTD 83 
                                           6************************************************************************ PP

                             TIGR01236  74 aveaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkya 146
                                           av aa++a   W e+pf++raa+fl+aadll+g+yr  i+aatmlgqsk++ qaeida++elidf+rfnv+ya
  NCBI__GCF_000504245.1:WP_034270111.1  84 AVTAAKEAAPAWREMPFDERAAVFLRAADLLAGPYRDTINAATMLGQSKSIQQAEIDAACELIDFLRFNVHYA 156
                                           ************************************************************************* PP

                             TIGR01236 147 relleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkil 219
                                           r +++ qP  s+pg++n++eyr+leGfv+ai+Pfnftaia+nl++aPalmGn+vvWkP+ t+ l+++ +m++l
  NCBI__GCF_000504245.1:WP_034270111.1 157 RRIYAEQP-NSVPGVWNRMEYRSLEGFVTAITPFNFTAIAGNLPTAPALMGNTVVWKPTPTQQLAAHFTMRVL 228
                                           ********.7*************************************************************** PP

                             TIGR01236 220 eeaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvl 292
                                           e+aGlPpgvin+v++dg +vs+v+lad+d+a+lhftGsta+fk lw+++ +nld+y+++PrivGetGGkdfv+
  NCBI__GCF_000504245.1:WP_034270111.1 229 EAAGLPPGVINMVTGDGKAVSEVALADPDFAGLHFTGSTATFKLLWRTIGENLDRYKHYPRIVGETGGKDFVI 301
                                           ************************************************************************* PP

                             TIGR01236 293 vhpsadveevvaatirgafeyqGqkcsaasrlyvpkslwke.lkeellaelkkvkvgdvddlssfmgavidek 364
                                           +hpsa+ +++v+a++rgafeyqGqkcsa+sr+y+++slw+  ++++l + +k + +gdv dls f gavid++
  NCBI__GCF_000504245.1:WP_034270111.1 302 AHPSARTDTLVTALVRGAFEYQGQKCSAVSRAYIARSLWEGgVRDQLADVTKTISYGDVSDLSHFGGAVIDAR 374
                                           ***************************************9548999*************************** PP

                             TIGR01236 365 sfakivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeil 437
                                           +fak + ++++   dp +l++l+GG +dds Gyfv Pt++ + dP+++++++e+fGP+ +vyvy+dd y e l
  NCBI__GCF_000504245.1:WP_034270111.1 375 AFAKHKALLDSVDGDP-ALDVLVGGGCDDSVGYFVDPTILVASDPNHEVFSKEYFGPICAVYVYEDDDYAEAL 446
                                           ****************.9******************************************************* PP

                             TIGR01236 438 evvdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillr 510
                                           ++vds++ yaltG vfa+dr+ai++a+ +l +aaGnfy+ndk+tG++vgqqpfGGar+sGtndkaG++ +l r
  NCBI__GCF_000504245.1:WP_034270111.1 447 RLVDSSAPYALTGGVFADDRDAIQQAHRALGYAAGNFYVNDKPTGSIVGQQPFGGARASGTNDKAGSMFNLQR 519
                                           ************************************************************************* PP

                             TIGR01236 511 fvsarsiketfkeltdfkypym 532
                                           + s+rsike+f+++td++yp+m
  NCBI__GCF_000504245.1:WP_034270111.1 520 WASPRSIKENFVAPTDHTYPHM 541
                                           *********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (542 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 36.48
//
[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 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