Alignments for a candidate for deoC in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoC in Herbaspirillum seropedicae SmR1

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate HSERO_RS05120 HSERO_RS05120 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__HerbieS:HSERO_RS05120
          Length = 343

 Score =  357 bits (915), Expect = e-103
 Identities = 183/303 (60%), Positives = 231/303 (76%), Gaps = 2/303 (0%)

Query: 11  DLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDTSSNIQR 70
           D +    +++N  A  +R   ++ RR+VKK+ QAAWLLKA+T IDLTTLSGDDT   ++R
Sbjct: 38  DAAAFEHLRINLSAAEKRVATLKGRRSVKKDAQAAWLLKAITCIDLTTLSGDDTPQRVRR 97

Query: 71  LCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVASVAAGFP 130
           LC KA  P+R DLL+AL M D+G+TT AVCVY   V  AV AL+  G  IPVA+V+ GFP
Sbjct: 98  LCAKAANPLRADLLEALGMQDRGLTTGAVCVYHRFVKTAVDALEGKG--IPVAAVSTGFP 155

Query: 131 AGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGEAHLKTI 190
           AG      +L+EI  +V DGA EID+VI R  VLTG WEALY E+R FR+ACGEAH+K I
Sbjct: 156 AGLNPHALKLKEIEASVRDGAAEIDIVITREHVLTGNWEALYREMRDFRQACGEAHVKAI 215

Query: 191 LATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFFWKTGNK 250
           LATGEL TL NV KASM+ MMAG+DFIKTSTGKE+VNAT  V++VMLR IR +   TG K
Sbjct: 216 LATGELKTLRNVAKASMVCMMAGADFIKTSTGKESVNATPLVSLVMLRMIRQYQEMTGIK 275

Query: 251 IGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHHVTGRYA 310
           +G+KPAGG+ +AKD L +  L+KEELG +WL+P+LFR+GAS+LL+DIERQ+ HHVTGRY+
Sbjct: 276 VGYKPAGGVATAKDVLEYQVLMKEELGHDWLQPDLFRVGASSLLADIERQLEHHVTGRYS 335

Query: 311 AYH 313
           A++
Sbjct: 336 AFN 338


Lambda     K      H
   0.320    0.133    0.397 

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: 342
Number of extensions: 10
Number of successful extensions: 2
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: 318
Length of database: 343
Length adjustment: 28
Effective length of query: 290
Effective length of database: 315
Effective search space:    91350
Effective search space used:    91350
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate HSERO_RS05120 HSERO_RS05120 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

# 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/TIGR00126.hmm
# target sequence database:        /tmp/gapView.8331.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00126  [M=211]
Accession:   TIGR00126
Description: deoC: deoxyribose-phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    2.7e-48  150.2   0.6    1.5e-47  147.8   0.6    1.9  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05120  HSERO_RS05120 deoxyribose-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05120  HSERO_RS05120 deoxyribose-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   0.6   1.5e-47   1.5e-47       4     205 ..      79     305 ..      76     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 1.5e-47
                                  TIGR00126   4 kliDhtalkadtteedietlcaeAkky................kfaavcvnpsyvslAkelLkgteve 55 
                                                + iD+t+l+ d+t++ + +lca+A ++                 + avcv+ ++v+ A++ L+g+ + 
  lcl|FitnessBrowser__HerbieS:HSERO_RS05120  79 TCIDLTTLSGDDTPQRVRRLCAKAANPlradllealgmqdrglTTGAVCVYHRFVKTAVDALEGKGIP 146
                                                68**********************9988888888787777776788********************** PP

                                  TIGR00126  56 ictv.vgFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKv 122
                                                +++v +gFP+G + +  kl E +++++ GA E+D+vi    +  +n+e+ +++++   +ac+++++K+
  lcl|FitnessBrowser__HerbieS:HSERO_RS05120 147 VAAVsTGFPAGLNPHALKLKEIEASVRDGAAEIDIVITREHVLTGNWEALYREMRDFRQACGEAHVKA 214
                                                ***978************************************************************** PP

                                  TIGR00126 123 ilEtalLtdeekk.kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasG 182
                                                il t++L+    + kAs +++ agadf+Ktstg+  ++At+    +m +++++       +vg K++G
  lcl|FitnessBrowser__HerbieS:HSERO_RS05120 215 ILATGELKTLRNVaKASMVCMMAGADFIKTSTGKESVNATPLVSLVMLRMIRQyqemtgiKVGYKPAG 282
                                                *******9876655**************************99988999999888999999******** PP

                                  TIGR00126 183 Gvrtaedalalieagaerigasa 205
                                                Gv ta+d+l++     e +g ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS05120 283 GVATAKDVLEYQVLMKEELGHDW 305
                                                *********99888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (343 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 3.89
//
[ok]

This GapMind analysis is from Sep 17 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 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