Alignments for a candidate for serA in Crocosphaera subtropica ATCC 51142

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Crocosphaera subtropica ATCC 51142

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_009546886.1 CCE_RS10125 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000017845.1:WP_009546886.1
          Length = 525

 Score =  445 bits (1145), Expect = e-129
 Identities = 234/525 (44%), Positives = 343/525 (65%), Gaps = 2/525 (0%)

Query: 1   MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           M+K+L++DP+ +  ++IL Q  +V+V TGL  EEL   I + DA+++RSGT  T+EII A
Sbjct: 1   MAKVLVSDPIDQVGIDILSQVAQVDVKTGLPPEELVKIIPEYDAMMLRSGTRVTKEIIAA 60

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
              LK+I RAGVGVDN+D+ AAT +GIVVVN+P+ ++I+ AE    MML+ +R+IP+A  
Sbjct: 61  GTQLKIIGRAGVGVDNIDVPAATRQGIVVVNSPEGNTIAAAEHALAMMLSLSRHIPEANQ 120

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
           S+K+ KW+RK F G EIY KTLG+VGLG+IG  VA  A++ GM ++AYDP+I ++ A +L
Sbjct: 121 SVKNNKWERKRFIGAEIYKKTLGVVGLGKIGSHVANVAKSMGMKLLAYDPFISKERADQL 180

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           G  L+ +D L   SD+ITLH+P TP+T H+I KE +  MK    I+NCARGG IDE AL 
Sbjct: 181 GCTLVDLDLLFAESDYITLHIPKTPETTHLINKEALGKMKPTARIINCARGGTIDEDALA 240

Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300
           +A+  GKI  AALDVFE+EP  ES L   +N+I TPH GAST EAQ++    VAEQ   +
Sbjct: 241 EAIAEGKIAGAALDVFEEEPLGESKLRNYDNIILTPHLGASTAEAQVNVAVDVAEQIRDV 300

Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360
           L G  A + VN+P +  + M+K++PY+ LAE +G++  Q     IE L +   G LA  K
Sbjct: 301 LLGLPARSAVNIPGLTPDVMEKMRPYLQLAETLGNLVGQLAGGRIERLTVRLQGELASTK 360

Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAE-GTMSESDYGNSIKISAKGEN 419
            + +  + +KG+L+  L   VN VNA + AK R ++I E    S  DY  S+ +SA+G  
Sbjct: 361 GQPIVVASIKGLLSQALRERVNYVNAAIEAKERGVRIIETRDASIRDYSGSLHLSAQGSL 420

Query: 420 DEISIIGS-IEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIA 478
            E S+ G+ +   E+   +++G+ +++ P   +    H D PG++GK+G LLG   +NIA
Sbjct: 421 GEHSVTGALLSDGEIRITDVDGFPINVPPSNYMLFTVHRDMPGIIGKIGSLLGSFNVNIA 480

Query: 479 GMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523
            MQVGR+   G ++M L +D  + + +L EI K+  +R A ++ +
Sbjct: 481 SMQVGRKIVRGDAVMALSLDDPLPEGLLTEITKVSGIRDAYTVKL 525


Lambda     K      H
   0.316    0.134    0.364 

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: 716
Number of extensions: 35
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: 523
Length of database: 525
Length adjustment: 35
Effective length of query: 488
Effective length of database: 490
Effective search space:   239120
Effective search space used:   239120
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_009546886.1 CCE_RS10125 (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.1979.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-225  734.5   2.3   4.1e-225  734.4   2.3    1.0  1  lcl|NCBI__GCF_000017845.1:WP_009546886.1  CCE_RS10125 phosphoglycerate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017845.1:WP_009546886.1  CCE_RS10125 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.4   2.3  4.1e-225  4.1e-225       1     525 []       3     525 .]       3     525 .] 0.99

  Alignments for each domain:
  == domain 1  score: 734.4 bits;  conditional E-value: 4.1e-225
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvlv+d++++ gi++l++ + +vdvktgl  eel+++i++yda+++RS t+vt+e+++a ++Lk+igRa
  lcl|NCBI__GCF_000017845.1:WP_009546886.1   3 KVLVSDPIDQVGIDILSQVA-QVDVKTGLPPEELVKIIPEYDAMMLRSGTRVTKEIIAAGTQLKIIGRA 70 
                                               7****************996.************************************************ PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvGvDNid++aat++Gi+vvN+Pegnti+aaE+ala++l+l+R+ip+a++svk++kWerk+f+G E+y+
  lcl|NCBI__GCF_000017845.1:WP_009546886.1  71 GVGVDNIDVPAATRQGIVVVNSPEGNTIAAAEHALAMMLSLSRHIPEANQSVKNNKWERKRFIGAEIYK 139
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlGv+GlG+iGs+va+ ak++gmk+layDP+is+e+a++lg++ l dld l+ae+D it+H+P+t+et
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 140 KTLGVVGLGKIGSHVANVAKSMGMKLLAYDPFISKERADQLGCT-LVDLDLLFAESDYITLHIPKTPET 207
                                               ********************************************.667********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                                +li+ke+l kmK++++i+NcaRGG idE+AL+ea+ egk+++aalDvfe+EP  ++kl + dn+++tp
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 208 THLINKEALGKMKPTARIINCARGGTIDEDALAEAIAEGKIAGAALDVFEEEPLGESKLRNYDNIILTP 276
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345
                                               HlgAst+Eaq nvav+vae+++++l g +++savN+p l+ +++ek++pyl+lae+lG+l++ql+++++
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 277 HLGASTAEAQVNVAVDVAEQIRDVLLGLPARSAVNIPGLTPDVMEKMRPYLQLAETLGNLVGQLAGGRI 345
                                               ********************************************************************* PP

                                 TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414
                                               ++++v l+Gela+++ ++++ a +kgll+++l+e+vn+vnA++ akerg+++ e+++++ +dy+ +l++
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 346 ERLTVRLQGELASTKGQPIVVASIKGLLSQALRERVNYVNAAIEAKERGVRIIETRDASIRDYSGSLHL 414
                                               ********************************************************************* PP

                                 TIGR01327 415 kveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmq 483
                                                ++++ ge+sv+g++l++ e ri+++dgf +++ p++++l++ ++D+pG+igk+gsllg++++Niasmq
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 415 SAQGSLGEHSVTGALLSDGEIRITDVDGFPINVPPSNYMLFTVHRDMPGIIGKIGSLLGSFNVNIASMQ 483
                                               ********************************************************************* PP

                                 TIGR01327 484 lgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                               +grk  +g+a+m lslD++++e++l+ei++v+ i+++++v+l
  lcl|NCBI__GCF_000017845.1:WP_009546886.1 484 VGRKIVRGDAVMALSLDDPLPEGLLTEITKVSGIRDAYTVKL 525
                                               ***************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (525 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.93
//
[ok]

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

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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