Alignments for a candidate for astE in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Paraburkholderia bryophila 376MFSha3.1

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate H281DRAFT_06483 H281DRAFT_06483 succinylglutamate desuccinylase

Query= reanno::BFirm:BPHYT_RS07720
         (342 letters)



>FitnessBrowser__Burk376:H281DRAFT_06483
          Length = 350

 Score =  592 bits (1526), Expect = e-174
 Identities = 293/338 (86%), Positives = 311/338 (92%)

Query: 5   LLDDFLAYTLAGTRPAASETQGTCAGGVRWSWLDDGVLLMEPAAQDESVRSVLVSAGVHG 64
           +LDDFLAYTLAGTRP+A+ET GTC GGVRWSWLD+GVLLMEPAA     RSVL SAGVHG
Sbjct: 13  MLDDFLAYTLAGTRPSANETHGTCGGGVRWSWLDEGVLLMEPAAITADTRSVLASAGVHG 72

Query: 65  DETAPIELLGFLVRDIAQGTAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRHLQVP 124
           DETAPIELL  LVRD+A+G AALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRHLQ+P
Sbjct: 73  DETAPIELLSHLVRDMARGEAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRHLQLP 132

Query: 125 QSYEAPRAAALEQAATQFFAAASNKSGARWHIDMHTAIRASAFEQFALLPHTGKPFSRAM 184
            SYEAPRAAALEQAATQFFA AS + GARWHIDMHTAIRASAFE+FALLPHTG+PFSRAM
Sbjct: 133 HSYEAPRAAALEQAATQFFATASRQPGARWHIDMHTAIRASAFERFALLPHTGRPFSRAM 192

Query: 185 FEWLGEARISAVLLHTTKGNTYSHFTAQVCGAEACTLELGKVRPFGQNDLTRFAGADHAV 244
           FEWL EARISAVLLHTTKGNTYSHFTAQ C AEACTLELGKVRPFGQNDLTRFAGAD A+
Sbjct: 193 FEWLAEARISAVLLHTTKGNTYSHFTAQACEAEACTLELGKVRPFGQNDLTRFAGADAAL 252

Query: 245 RHLLAGMRGHVRADLPRAFTVIDQITKQSDAFELLVAADVANFTPFAKGTVLARDGEYRY 304
           RHLLAG  G  +A+LPRAFTVIDQITK S+AFELLVA DVANFTPF KGT+LARDG+YRY
Sbjct: 253 RHLLAGTSGREQAELPRAFTVIDQITKPSEAFELLVAPDVANFTPFGKGTLLARDGDYRY 312

Query: 305 VVQHDEERLVFPNATVKPGLRAGLMVVETTQDTLSKLV 342
           VVQHDEERLVFPNATVKPGLRAGLMV+ETT DTL+KLV
Sbjct: 313 VVQHDEERLVFPNATVKPGLRAGLMVIETTHDTLAKLV 350


Lambda     K      H
   0.322    0.135    0.403 

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: 482
Number of extensions: 8
Number of successful extensions: 1
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: 342
Length of database: 350
Length adjustment: 29
Effective length of query: 313
Effective length of database: 321
Effective search space:   100473
Effective search space used:   100473
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_06483 H281DRAFT_06483 (succinylglutamate desuccinylase)
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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/TIGR03242.hmm
# target sequence database:        /tmp/gapView.31364.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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-128  414.3   0.0     2e-128  414.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06483  H281DRAFT_06483 succinylglutamat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06483  H281DRAFT_06483 succinylglutamate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.1   0.0    2e-128    2e-128       1     318 [.      16     338 ..      16     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 414.1 bits;  conditional E-value: 2e-128
                                    TIGR03242   1 dflaltlekkepevtqge...aknvklrwldeGvlelePe..aeaekslvisaGihGnetaPiell 61 
                                                  dfla tl+  +p++++++     +v++ wldeGvl +eP+  +  ++s++ saG+hG+etaPiell
  lcl|FitnessBrowser__Burk376:H281DRAFT_06483  16 DFLAYTLAGTRPSANETHgtcGGGVRWSWLDEGVLLMEPAaiTADTRSVLASAGVHGDETAPIELL 81 
                                                  79********99776665446679****************888899******************** PP

                                    TIGR03242  62 eqllsdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvv 127
                                                  ++l++d+a+g+ +l +rlL+ilGn  a+r + Ry ++dlnRlf+Gr+ +l +s e+ Ra+ Leq++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06483  82 SHLVRDMARGEAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRHLQLPHSYEAPRAAALEQAA 147
                                                  ****************************************************************** PP

                                    TIGR03242 128 eaffeagkasea.ryhyDlhtaiRasklekfallPyqekpfdkellewlaaadldavllhkekggt 192
                                                  ++ff++++++   r+h+D+htaiRas +e+fallP++++pf+++++ewla+a + avllh++kg+t
  lcl|FitnessBrowser__Burk376:H281DRAFT_06483 148 TQFFATASRQPGaRWHIDMHTAIRASAFERFALLPHTGRPFSRAMFEWLAEARISAVLLHTTKGNT 213
                                                  *****99887645***************************************************** PP

                                    TIGR03242 193 fshfssekleaeactlelGkarPfGendlsqfqaitealralisdeaiparkkeelklfevvesil 258
                                                  +shf+++++eaeactlelGk+rPfG+ndl++f+ +++alr l+++++  ++ + + ++f+v+++i+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06483 214 YSHFTAQACEAEACTLELGKVRPFGQNDLTRFAGADAALRHLLAGTSGREQAELP-RAFTVIDQIT 278
                                                  *******************************************998888777777.9********* PP

                                    TIGR03242 259 kksdsfelhvaedasnftefakGtllaedkderyrveeeeerilfPnakvanGlRaglll 318
                                                  k s++fel va d+ nft+f kGtlla+d d+ry+v+++eer++fPna+v+ GlRagl++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06483 279 KPSEAFELLVAPDVANFTPFGKGTLLARDGDYRYVVQHDEERLVFPNATVKPGLRAGLMV 338
                                                  ***********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (350 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: 8.42
//
[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