Alignments for a candidate for serA in Dehalococcoides mccartyi 195

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Dehalococcoides mccartyi 195

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_010936374.1 DET_RS03170 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_000011905.1:WP_010936374.1
          Length = 526

 Score =  407 bits (1047), Expect = e-118
 Identities = 223/526 (42%), Positives = 329/526 (62%), Gaps = 2/526 (0%)

Query: 1   MFRVLVSDKMSNDGLQPLIESDFIEI-VQKNVADAEDELHTFDALLVRSATKVTEDLFNK 59
           M +VLVSD +S  GL PL E   +++       +    +  +DALLVRS T+VT D+ N 
Sbjct: 1   MKKVLVSDALSATGLSPLKEIAQVDVKTGLKPEELVSIIGEYDALLVRSQTQVTADIINA 60

Query: 60  MTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANI 119
              L+++GRAGVGVDNID+  AT +G+IV+NAP GNTIS  EHT A++ S+ RHIP+AN 
Sbjct: 61  GKKLQVIGRAGVGVDNIDLKAATGNGIIVVNAPTGNTISATEHTLALMLSMARHIPRANA 120

Query: 120 SVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKI 179
           S+KS +W R  +VGSEL GKTLGIVGLG IGSEIA+R  A  M V  +DPF++ ERAKK+
Sbjct: 121 SLKSGQWKRNEFVGSELKGKTLGIVGLGNIGSEIAKRALALEMRVIGYDPFISMERAKKL 180

Query: 180 GVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALL 239
            V    FE++L+ AD IT+H P+T +TKGL+  + +   K  VRLIN +RGGIIDE AL 
Sbjct: 181 QVELVPFEDLLKQADFITLHVPMTGQTKGLIGPKELEMMKPTVRLINTSRGGIIDEEALA 240

Query: 240 EALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQF 299
            A+    + GAA+DVF  EP  ++ L +   +I TPHLGAST EAQ    + V ++V+  
Sbjct: 241 AAIREKRIGGAAIDVFSKEPCTESCLFECDNIIVTPHLGASTAEAQELATSDVVKQVIDV 300

Query: 300 AKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKLE 359
            +G P   A+N P ++ +    + P+  +A  +GSLVSQ     +++V I+Y G +A  +
Sbjct: 301 FEGRPARYAVNAPYISAESLPVVGPFMPVARTVGSLVSQLTDGHMKNVTIKYCGELAAYD 360

Query: 360 TSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGDR 419
           T+ +   +L G L+   +  VN VNA  VA +RG+  +E+  S+   + + I+V +  D 
Sbjct: 361 TTALKALVLGGILEHISEERVNVVNADIVAAQRGLGVTEQKESACQNFSSLITVTIDTDN 420

Query: 420 STFTVTATYIPHFGERIVEINGFNIDFYPT-GHLVYIQHQDTTGVIGRVGRILGDNDINI 478
                 A  +      IV +N + ID  PT G+ ++  H D  G+IG  G+I GD DINI
Sbjct: 421 GKSNTVAGSLVRGDVHIVRLNDYWIDIVPTGGYFLFADHIDRPGLIGAAGKITGDADINI 480

Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524
           + M + R++  G+A+M+L+ D  L +K  ++L ++PD+ +V+++ +
Sbjct: 481 SYMHLSRQKARGQALMILALDEPLPEKQRQQLLSLPDVQTVQVVKI 526


Lambda     K      H
   0.317    0.134    0.374 

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: 664
Number of extensions: 21
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: 525
Length of database: 526
Length adjustment: 35
Effective length of query: 490
Effective length of database: 491
Effective search space:   240590
Effective search space used:   240590
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_010936374.1 DET_RS03170 (phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

# 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.aa/TIGR01327.hmm
# target sequence database:        /tmp/gapView.9430.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01327  [M=525]
Accession:   TIGR01327
Description: PGDH: phosphoglycerate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.2e-200  651.8   3.2   4.8e-200  651.7   3.2    1.0  1  lcl|NCBI__GCF_000011905.1:WP_010936374.1  DET_RS03170 phosphoglycerate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000011905.1:WP_010936374.1  DET_RS03170 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.7   3.2  4.8e-200  4.8e-200       1     525 []       3     526 .]       3     526 .] 0.98

  Alignments for each domain:
  == domain 1  score: 651.7 bits;  conditional E-value: 4.8e-200
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvlv+d ls++g+  lke + +vdvktgl+ eel+++i +ydal+vRS+t+vt+++++a +kL+vigRa
  lcl|NCBI__GCF_000011905.1:WP_010936374.1   3 KVLVSDALSATGLSPLKEIA-QVDVKTGLKPEELVSIIGEYDALLVRSQTQVTADIINAGKKLQVIGRA 70 
                                               7*************999775.9*********************************************** PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvGvDNid++aat  Gi+vvNaP+gntisa+E++lal+l++aR+ip+a++s+k+++W+r++f+G+El+g
  lcl|NCBI__GCF_000011905.1:WP_010936374.1  71 GVGVDNIDLKAATGNGIIVVNAPTGNTISATEHTLALMLSMARHIPRANASLKSGQWKRNEFVGSELKG 139
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlG++GlG+iGse+akra al+m+v++yDP+is e+a+kl vel   +++ll++aD+it+HvP t +t
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 140 KTLGIVGLGNIGSEIAKRALALEMRVIGYDPFISMERAKKLQVEL-VPFEDLLKQADFITLHVPMTGQT 207
                                               ********************************************5.55********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                               kglig +el+ mK++v+++N++RGGiidE+AL+ a+ e+++ +aa+Dvf+kEP+t++ l+e dn++vtp
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 208 KGLIGPKELEMMKPTVRLINTSRGGIIDEEALAAAIREKRIGGAAIDVFSKEPCTESCLFECDNIIVTP 276
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345
                                               HlgAst+Eaqe ++ +v+++v+++ +g ++++avN+p ++ae+l  + p++ +a+++G+l+sql+++++
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 277 HLGASTAEAQELATSDVVKQVIDVFEGRPARYAVNAPYISAESLPVVGPFMPVARTVGSLVSQLTDGHM 345
                                               ********************************************************************* PP

                                 TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414
                                               k+v+++++Gela++++ +l++ +l g+l+++ ee+vn+vnA +va++rg+ v+e+ke++ +++++l++v
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 346 KNVTIKYCGELAAYDTTALKALVLGGILEHISEERVNVVNADIVAAQRGLGVTEQKESACQNFSSLITV 414
                                               ********************************************************************* PP

                                 TIGR01327 415 kveadkg.evsvagtvleekepriveidgfevdlepeg.illiiknkDkpGvigkvgsllgeagiNias 481
                                               ++ +d+g + +vag+++     +iv+++++ +d+ p+g + l++ + D+pG+ig  g++ g+a+iNi  
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 415 TIDTDNGkSNTVAGSLVR-GDVHIVRLNDYWIDIVPTGgYFLFADHIDRPGLIGAAGKITGDADINISY 482
                                               ****99856789999999.599*************986378999************************* PP

                                 TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                               m+l+r++++g+alm+l lDe+++e++ +++ ++p++++v++v++
  lcl|NCBI__GCF_000011905.1:WP_010936374.1 483 MHLSRQKARGQALMILALDEPLPEKQRQQLLSLPDVQTVQVVKI 526
                                               *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (526 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: 00:00:00.03
# Mc/sec: 7.54
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Steps (tab-delimited)
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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis