Alignments for a candidate for astC in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astC in Halomonas desiderata SP1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_086508150.1 BZY95_RS01045 aspartate aminotransferase family protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_002151265.1:WP_086508150.1
          Length = 404

 Score =  528 bits (1360), Expect = e-154
 Identities = 256/402 (63%), Positives = 314/402 (78%)

Query: 1   MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60
           MS + TR++FD++M+P Y+P   IPVRGEGSRLWDQ+G+EYIDFAGGIAVN+LGH HP L
Sbjct: 1   MSHTPTRADFDQYMVPNYSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVL 60

Query: 61  VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120
           VKALTEQ  K WH  N YTNEP L+LAK L++ TFAD+ +FC+SG EANEAALKLAR++A
Sbjct: 61  VKALTEQGNKLWHLSNVYTNEPSLKLAKTLVERTFADKAYFCSSGGEANEAALKLARRWA 120

Query: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180
           HD FG  K  IV+F  +FHGRT FTVS GGQP YSQ F P+P  I H  +N+LDS + LI
Sbjct: 121 HDNFGEHKHRIVSFYQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLI 180

Query: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240
           +D+TCAV+VEPMQGEGG+ PA  +FL+GLR+LCDAH+ALLIFDEVQTGVGRTG LYAYM 
Sbjct: 181 NDDTCAVMVEPMQGEGGITPATQEFLQGLRDLCDAHDALLIFDEVQTGVGRTGSLYAYME 240

Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300
           YG+ PD+L++AKALGGGFPIGA+L ++R A  + +GTHG+TYGGN LA AVA      I+
Sbjct: 241 YGIEPDILTSAKALGGGFPIGAMLTTDRVAPALAIGTHGSTYGGNALASAVALAAVEHID 300

Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360
           T EVL GVKQRH  F E L AIN ++G+F+EIRG+GLLIG  +  EY  +AK I   A E
Sbjct: 301 TPEVLGGVKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDRAKDILPLAIE 360

Query: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLA 402
           EGLM LIAG NV+R AP+L+I E ++  G+ R E A +R +A
Sbjct: 361 EGLMALIAGPNVLRMAPSLVIPEADIAEGMARLERAIERLVA 402


Lambda     K      H
   0.321    0.137    0.412 

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: 527
Number of extensions: 22
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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: 50 (23.9 bits)

Align candidate WP_086508150.1 BZY95_RS01045 (aspartate aminotransferase family protein)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

# 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/TIGR03246.hmm
# target sequence database:        /tmp/gapView.12118.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03246  [M=397]
Accession:   TIGR03246
Description: arg_catab_astC: succinylornithine transaminase family
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-213  695.3   0.0   1.3e-213  695.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508150.1  BZY95_RS01045 aspartate aminotra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508150.1  BZY95_RS01045 aspartate aminotransferase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.2   0.0  1.3e-213  1.3e-213       2     397 .]       6     401 ..       5     401 .. 1.00

  Alignments for each domain:
  == domain 1  score: 695.2 bits;  conditional E-value: 1.3e-213
                                 TIGR03246   2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhl 70 
                                               +r++fd++mvp+y+p k+ipvrgeGsr+wdqeg+eyidfaGGiavn+lGh+hp lv+al+eq++klwhl
  lcl|NCBI__GCF_002151265.1:WP_086508150.1   6 TRADFDQYMVPNYSPQKVIPVRGEGSRLWDQEGREYIDFAGGIAVNSLGHCHPVLVKALTEQGNKLWHL 74 
                                               699****************************************************************** PP

                                 TIGR03246  71 gngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtl 139
                                               +n+ytnep l+lak lv+ tfadk++fc sG+eaneaalklar++a+d++g++k+ iv+f +sfhGrt+
  lcl|NCBI__GCF_002151265.1:WP_086508150.1  75 SNVYTNEPSLKLAKTLVERTFADKAYFCSSGGEANEAALKLARRWAHDNFGEHKHRIVSFYQSFHGRTF 143
                                               ********************************************************************* PP

                                 TIGR03246 140 ftvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrel 208
                                               ftvsvGGq+kys++f+p+p+gi h ++n+l+++++li+d+tcav+vep+qGegG++pa+++fl+glr+l
  lcl|NCBI__GCF_002151265.1:WP_086508150.1 144 FTVSVGGQPKYSQGFGPVPGGIVHGEFNNLDSVRDLINDDTCAVMVEPMQGEGGITPATQEFLQGLRDL 212
                                               ********************************************************************* PP

                                 TIGR03246 209 cdrhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGtt 277
                                               cd+h+allifdevqtGvGrtG+lyaymeyG++pdiltsakalGgGfpiGa+ltt+++a +l++GthG+t
  lcl|NCBI__GCF_002151265.1:WP_086508150.1 213 CDAHDALLIFDEVQTGVGRTGSLYAYMEYGIEPDILTSAKALGGGFPIGAMLTTDRVAPALAIGTHGST 281
                                               ********************************************************************* PP

                                 TIGR03246 278 yGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGk 346
                                               yGGn la+ava + ++ ++t+e+l Gvkqrh+lf ++le+in+++ vf+eirG+GlliGa++t ey+ +
  lcl|NCBI__GCF_002151265.1:WP_086508150.1 282 YGGNALASAVALAAVEHIDTPEVLGGVKQRHDLFREHLEAINRKHGVFREIRGMGLLIGAEMTPEYKDR 350
                                               ********************************************************************* PP

                                 TIGR03246 347 akdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekaveklv 397
                                               akd++ +a eeG+++liaGp+v+r+apslvi+e++i+eG+arle+a+e+lv
  lcl|NCBI__GCF_002151265.1:WP_086508150.1 351 AKDILPLAIEEGLMALIAGPNVLRMAPSLVIPEADIAEGMARLERAIERLV 401
                                               ************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (397 nodes)
Target sequences:                          1  (404 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: 10.92
//
[ok]

This GapMind analysis is from Sep 24 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