Alignments for a candidate for gabT in Sphingomonas histidinilytica UM2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Sphingomonas histidinilytica UM2

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_079648324.1 B5X82_RS11660 4-aminobutyrate--2-oxoglutarate transaminase

Query= BRENDA::Q0K2K2
         (423 letters)



>NCBI__GCF_900167915.1:WP_079648324.1
          Length = 434

 Score =  479 bits (1233), Expect = e-140
 Identities = 247/426 (57%), Positives = 301/426 (70%), Gaps = 4/426 (0%)

Query: 1   MTMKNLELNQRRTLATPRGVGVMCDFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRH 60
           +T  N  L  RR  A P GV      +A RAENA +WDVEGR Y DFA+GIAVLN GHRH
Sbjct: 5   LTSSNDTLWDRRLAAVPHGVATAAPIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRH 64

Query: 61  PRVMQAIAAQLERFTHTAYQIVPYQGYVTLAERINALVPIQGLNKTALFTTGAEAVENAI 120
           PR++ A+  QL RFTHTA+Q+V Y+ YV LAER+NAL P+ G  KT  FTTGAEA ENA+
Sbjct: 65  PRIIAAVEEQLGRFTHTAFQVVGYEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAV 124

Query: 121 KIARAHTGRPGVIAFSGAFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVS 180
           KIAR  +GR  VIAF   FHGRTLL  A+TGKV PYK GFGP P DIYH PFPS  HGV+
Sbjct: 125 KIARYASGRSAVIAFVNGFHGRTLLASAMTGKVLPYKKGFGPLPGDIYHIPFPSEAHGVT 184

Query: 181 TERALQALEGLFKTDIDPARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIAD 240
            E +L AL  +  +D++ A VAAII+EPVQGEGGF  AP  F+R LR++CD+HGI LIAD
Sbjct: 185 VEHSLAALANILSSDVEAANVAAIILEPVQGEGGFHVAPFTFLRALRSLCDEHGIALIAD 244

Query: 241 EVQTGFGRTGKMFAMSHHDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYA 300
           EVQTG GRTGK+FA+ H  V PDLIT+AKSL GG PLSAV G AA++D   PGGLGGTYA
Sbjct: 245 EVQTGIGRTGKLFAVEHAGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLGGTYA 304

Query: 301 GNPLAVAAAHAVIDVIEEEKLCERSASLGQQLREHL--LAQRKHCPAMAEVRGLGSMVAA 358
           G+P+A AA  AV+DVIE++ LC+R+  +G+++ E L  +A R+  P +   RGLG+M+A 
Sbjct: 305 GSPIACAAGLAVLDVIEQDGLCDRAERMGRRITERLGAIAARRELP-IGMPRGLGAMIAF 363

Query: 359 EF-CDPATGQPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVL 417
           +        +P    AKRV  RALE GL+LLTCG +G  IR L PLT   A  D  L +L
Sbjct: 364 DIRAGLEDLRPDGGAAKRVCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDIL 423

Query: 418 TQALAE 423
            +ALA+
Sbjct: 424 ARALAD 429


Lambda     K      H
   0.321    0.136    0.400 

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: 585
Number of extensions: 26
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: 423
Length of database: 434
Length adjustment: 32
Effective length of query: 391
Effective length of database: 402
Effective search space:   157182
Effective search space used:   157182
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: 51 (24.3 bits)

Align candidate WP_079648324.1 B5X82_RS11660 (4-aminobutyrate--2-oxoglutarate transaminase)
to HMM TIGR00700 (gabT: 4-aminobutyrate transaminase (EC 2.6.1.19))

# 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/TIGR00700.hmm
# target sequence database:        /tmp/gapView.887679.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00700  [M=420]
Accession:   TIGR00700
Description: GABAtrnsam: 4-aminobutyrate transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-172  560.2   2.5   1.4e-172  560.0   2.5    1.0  1  NCBI__GCF_900167915.1:WP_079648324.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900167915.1:WP_079648324.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.0   2.5  1.4e-172  1.4e-172       2     420 .]      15     429 ..      14     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 560.0 bits;  conditional E-value: 1.4e-172
                             TIGR00700   2 rraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafqvvp 74 
                                           rr+aav++Gv+++++++aa+ae+ae+ dv+G+r+id+a+giavlnvGh+hP++++av++q+ ++thtafqvv 
  NCBI__GCF_900167915.1:WP_079648324.1  15 RRLAAVPHGVATAAPIFAARAENAEIWDVEGRRYIDFASGIAVLNVGHRHPRIIAAVEEQLGRFTHTAFQVVG 87 
                                           9************************************************************************ PP

                             TIGR00700  75 yesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmaltakvkPy 147
                                           ye yv lae+lna+aP+ g++k++++++Gaea enavkiar  +gr +v+af +gfhGrt l+ a+t+kv Py
  NCBI__GCF_900167915.1:WP_079648324.1  88 YEPYVRLAERLNALAPVVGPAKTIFFTTGAEATENAVKIARYASGRSAVIAFVNGFHGRTLLASAMTGKVLPY 160
                                           ************************************************************************* PP

                             TIGR00700 148 kiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfivpakelv 220
                                           k GfGP+++++y++P+p++ ++ ++      +  laa+ ++  +dvea +vaa++lePvqGeGGf v++  ++
  NCBI__GCF_900167915.1:WP_079648324.1 161 KKGFGPLPGDIYHIPFPSEAHGVTV------EHSLAALANILSSDVEAANVAAIILEPVQGEGGFHVAPFTFL 227
                                           ********************99988......44577************************************* PP

                             TIGR00700 221 aavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeildapapGglG 293
                                            a++slc+ehgi liadevqtG  rtGklfa+eh +++Pdlitvaksl +G+Pls+vvG+a ++d   pGglG
  NCBI__GCF_900167915.1:WP_079648324.1 228 RALRSLCDEHGIALIADEVQTGIGRTGKLFAVEHAGVRPDLITVAKSLGGGFPLSAVVGNAALIDRVPPGGLG 300
                                           ************************************************************************* PP

                             TIGR00700 294 GtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevp.aigdvrglGamiavelv.dpdtte 364
                                           GtyaG+P+a+aa lavld+ie++gl++rae++g++++++l  + +  +  ig  rglGamia ++    +   
  NCBI__GCF_900167915.1:WP_079648324.1 301 GTYAGSPIACAAGLAVLDVIEQDGLCDRAERMGRRITERLGAIAARRElPIGMPRGLGAMIAFDIRaGLEDLR 373
                                           ***************************************987766555259**************96778999 PP

                             TIGR00700 365 PdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaalad 420
                                           Pd + a+++  +al+ Gl+llt+G +G+ irll+Plt sd+ ldegl+il  alad
  NCBI__GCF_900167915.1:WP_079648324.1 374 PDGGAAKRVCVRALELGLILLTCGQHGEAIRLLAPLTASDAVLDEGLDILARALAD 429
                                           ****************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (434 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: 31.35
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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