Alignments for a candidate for gabT in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for gabT in Klebsiella michiganensis M5al

Align 4-aminobutyrate aminotransferase PuuE; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; EC 2.6.1.19 (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein

Query= SwissProt::P50457
         (421 letters)



>FitnessBrowser__Koxy:BWI76_RS26375
          Length = 421

 Score =  651 bits (1679), Expect = 0.0
 Identities = 317/419 (75%), Positives = 362/419 (86%)

Query: 1   MSNNEFHQRRLSATPRGVGVMCNFFAQSAENATLKDVEGNEYIDFAAGIAVLNTGHRHPD 60
           M ++E +QRR  ATPRGVGVMC++F + AENATL D+EGNE IDFAAGIAVLNTGHRHP 
Sbjct: 1   MKSSELNQRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPK 60

Query: 61  LVAAVEQQLQQFTHTAYQIVPYESYVTLAEKINALAPVSGQAKTAFFTTGAEAVENAVKI 120
           ++AAVEQQLQ FTHTAYQIVPYESYVTLAE+INALAP+ G AKTAFFTTGAEAVENAVKI
Sbjct: 61  IIAAVEQQLQAFTHTAYQIVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKI 120

Query: 121 ARAHTGRPGVIAFSGGFHGRTYMTMALTGKVAPYKIGFGPFPGSVYHVPYPSDLHGISTQ 180
           ARA+TGRPG+I F GGFHGRT+MTMALTGKVAPYKIGFGPFPGSVYH  YP+  HGI+T 
Sbjct: 121 ARAYTGRPGLITFGGGFHGRTFMTMALTGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTA 180

Query: 181 DSLDAIERLFKSDIEAKQVAAIIFEPVQGEGGFNVAPKELVAAIRRLCDEHGIVMIADEV 240
           D++ +++R+FK+DI A QVAAI+ EP+QGEGGFNVAP E + A+R LCD HGI++IADEV
Sbjct: 181 DAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFNVAPPEFMQALRALCDTHGILLIADEV 240

Query: 241 QSGFARTGKLFAMDHYADKPDLMTMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGN 300
           Q+GFARTGKLFAM HY  KPDLMTMAKSLAGG PLSGVVG A +MDAPAPGGLGGTYAGN
Sbjct: 241 QTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVMDAPAPGGLGGTYAGN 300

Query: 301 PLAVAAAHAVLNIIDKESLCERANQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEFND 360
           PLAVAAAHAVL++I++E LC+RA +LG  LK  L  A++S PAIA VRG GSM+AVEFND
Sbjct: 301 PLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAVEFND 360

Query: 361 PQTGEPSAAIAQKIQQRALAQGLLLLTCGAYGNVIRFLYPLTIPDAQFDAAMKILQDAL 419
           PQTGEPSA I ++IQQ+A   GLLLL+CG YGNVIRFLYPLTIPDAQF  A+ IL   L
Sbjct: 361 PQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419


Lambda     K      H
   0.319    0.134    0.388 

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: 658
Number of extensions: 17
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: 421
Length of database: 421
Length adjustment: 32
Effective length of query: 389
Effective length of database: 389
Effective search space:   151321
Effective search space used:   151321
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 BWI76_RS26375 BWI76_RS26375 (aspartate aminotransferase family protein)
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.3385.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-207  675.3   3.0   1.5e-207  675.2   3.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS26375  BWI76_RS26375 aspartate aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS26375  BWI76_RS26375 aspartate aminotransferase family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  675.2   3.0  1.5e-207  1.5e-207       1     418 [.       8     419 ..       8     421 .] 0.99

  Alignments for each domain:
  == domain 1  score: 675.2 bits;  conditional E-value: 1.5e-207
                               TIGR00700   1 qrraaavskGvgvtlrvlaakaegaelkdvdGnrlidlaagiavlnvGhshPkvveavkrqveelthtafq 71 
                                             qrr++a+++Gvgv++++++ kae+a+l d++Gn+ id+aagiavln+Gh+hPk+++av++q++ +thta+q
  lcl|FitnessBrowser__Koxy:BWI76_RS26375   8 QRRQQATPRGVGVMCSYFVEKAENATLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQLQAFTHTAYQ 78 
                                             89********************************************************************* PP

                               TIGR00700  72 vvpyesyvelaeklnaiaPgsgekkavllnsGaeavenavkiarkytgrpgvvafsrgfhGrtnltmalta 142
                                             +vpyesyv+lae++na+aP  g++k++++++Gaeavenavkiar+ytgrpg+++f +gfhGrt++tmalt+
  lcl|FitnessBrowser__Koxy:BWI76_RS26375  79 IVPYESYVTLAERINALAPIDGPAKTAFFTTGAEAVENAVKIARAYTGRPGLITFGGGFHGRTFMTMALTG 149
                                             *********************************************************************** PP

                               TIGR00700 143 kvkPykiGfGPfapevyraPlpydyrdialdkqeslddelaaiealfvadveaeqvaavvlePvqGeGGfi 213
                                             kv+PykiGfGPf+++vy+a +p   ++i++       d +++++++f+ad++a+qvaa+vleP+qGeGGf+
  lcl|FitnessBrowser__Koxy:BWI76_RS26375 150 KVAPYKIGFGPFPGSVYHAVYPNAAHGITT------ADAMKSLDRIFKADIAADQVAAIVLEPIQGEGGFN 214
                                             ***************************998......3456799**************************** PP

                               TIGR00700 214 vpakelvaavaslckehgivliadevqtGfartGklfaieheddkPdlitvaksladGlPlsgvvGraeil 284
                                             v++ e+++a++ lc+ hgi+liadevqtGfartGklfa++h+d+kPdl+t+aksla+G+PlsgvvGrae++
  lcl|FitnessBrowser__Koxy:BWI76_RS26375 215 VAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPDLMTMAKSLAGGFPLSGVVGRAEVM 285
                                             *********************************************************************** PP

                               TIGR00700 285 dapapGglGGtyaGnPlavaaalavldiieeeglieraeqigklvkdklielkeevpaigdvrglGamiav 355
                                             dapapGglGGtyaGnPlavaaa+avld+ieee l++rae++g  +k+ l +++++ pai+dvrg+G+m+av
  lcl|FitnessBrowser__Koxy:BWI76_RS26375 286 DAPAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQRAERLGSHLKEVLNQARQSCPAIADVRGQGSMVAV 356
                                             *********************************************************************** PP

                               TIGR00700 356 elvdpdttePdaalaekiaaaalaaGlllltaGifGniirlltPltisdelldeglkileaal 418
                                             e++dp+t+eP+a ++++i+++a+++Gllll++G++Gn+ir+l+Plti+d+++ ++l+il  +l
  lcl|FitnessBrowser__Koxy:BWI76_RS26375 357 EFNDPQTGEPSAEITRQIQQKAQENGLLLLSCGVYGNVIRFLYPLTIPDAQFTKALDILARVL 419
                                             ***********************************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (420 nodes)
Target sequences:                          1  (421 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: 6.31
//
[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