Alignments for a candidate for put1 in Methylomicrobium alcaliphilum 20Z

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Methylomicrobium alcaliphilum 20Z

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_014148206.1 MEALZ_RS08415 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::SB2B:6938573
         (1058 letters)



>NCBI__GCF_000968535.2:WP_014148206.1
          Length = 1036

 Score =  989 bits (2557), Expect = 0.0
 Identities = 530/1041 (50%), Positives = 698/1041 (67%), Gaps = 16/1041 (1%)

Query: 16   NLDELFSLISQNYIVDEEAYLKELIALVPSSDEEIARITSRAHDLVAKVRQYEKKGLMVG 75
            +L  L   I Q Y+ DE A + EL  +V  +D   A   + A  LV ++R  + K  +V 
Sbjct: 5    SLSTLRKAIDQAYLNDETASVIEL--MVGLTDYNPAEAEALARLLVEQIRADKDKQSVV- 61

Query: 76   IDAFLQQYSLETQEGIILMCLAEALLRIPDAETADALIADKLSGAKWDEHMSKSDSVLVN 135
             DAF+ +Y L ++EG++LM +AEALLRIPD+ T D  +ADKLS A W  H+  SDS+LVN
Sbjct: 62   -DAFMHEYRLNSEEGVVLMSIAEALLRIPDSATQDRFLADKLSSADWQTHLHHSDSMLVN 120

Query: 136  ASTWGLMLTGKIVQLDKNLDGTPSNLLSRLVNRLGEPVIRQAMYAAMKIMGKQFVLGRTI 195
             ST  L++TG     ++ +    + +   L+ RLG+PVIR A+  AM  +G QFV+  TI
Sbjct: 121  LSTGALLVTGLF---ERYIKADEAQVFEYLLGRLGQPVIRLALQKAMHFLGSQFVMAETI 177

Query: 196  EEGLKNAAEKRKLGYTHSYDMLGEAALTMKDADKYYRDYANAIQALGTAKFDESEAPRPT 255
             E L   A ++   Y +S+DMLGEAA+T  DA++Y+  Y +AI+ L      ES   +P 
Sbjct: 178  FEALH--ASQKYSEYRYSFDMLGEAAVTASDAERYFSAYLDAIRQLSQESDGESLFEKPG 235

Query: 256  ISIKLSALHPRYEVANEDRVMTELYATLIKLIEQARSLNVGIQIDAEEVDRLELSLKLFK 315
            +S+KLSAL PRYE     R   EL A L+ L + AR   + + +DAEE +RL LSL +F+
Sbjct: 236  VSVKLSALCPRYEALQHQRATPELTAKLLTLAQYARQGGLTLTVDAEESERLSLSLTIFE 295

Query: 316  KLYQSDAAKGWGLLGIVVQAYSKRALPVLMWLTRLAKEQGDEIPLRLVKGAYWDSELKWA 375
             ++   + KGW  LG+ VQAY KRA  V+ WL+ LAK +  +IP+RLVKGAYWD+E+K  
Sbjct: 296  AVFTHPSLKGWPGLGLAVQAYQKRAPHVIAWLSALAKTEHKKIPVRLVKGAYWDTEIKRD 355

Query: 376  QQAGEAGYPLFTRKAATDVSYLACARYLLSEATRGVIYPQFASHNAQTVAAITAMVGDRK 435
            Q+ G  GYP+FTRK+ATD+SYLACA  LL E    + YPQFA+HNA TVAAI  M G+RK
Sbjct: 356  QEQGLTGYPVFTRKSATDISYLACATRLLIEPD--IFYPQFATHNAHTVAAIRQMAGNRK 413

Query: 436  -FEFQRLHGMGQELYDTVLAEA--AVPTVRIYAPIGAHKDLLPYLVRRLLENGANTSFVH 492
             +EFQRLHGMG+ LY  +      ++P  RIYAPIG +++LLPYLVRRLLENGANTSFV+
Sbjct: 414  DYEFQRLHGMGEALYQNLATHPNWSIPC-RIYAPIGHYQELLPYLVRRLLENGANTSFVN 472

Query: 493  KLVDPKTPIESLVTHPLKTLQGYKTLANNKIVKPADIFGAERKNSKGLNMNIISESEPFF 552
            ++ +P   IE +V +P+    G        +  P D+FG ER+NS+G N+    +     
Sbjct: 473  QIENPDIDIERIVQNPVSFWLGLNDFEKTSVPLPVDLFGKERRNSEGFNLADTEQLYSLQ 532

Query: 553  AALEKFKDTQWSAGPLVNGETLSGEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKA 612
             +L++       AGPL+NG+ LSG  R +V+P N + KVG VAF    T+  A+  A KA
Sbjct: 533  KSLDELSGLSHHAGPLINGKCLSGSERVIVNPANHSHKVGTVAFCGADTVADALDTASKA 592

Query: 613  FASWCRTPVETRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYA 672
            F +W  T V+ RA  L   ADLLE NR EL++LC  E G++I+D + +VREAVDFCRYYA
Sbjct: 593  FDAWRSTNVQKRARYLNNAADLLEYNRTELVSLCVSEGGRTIKDALADVREAVDFCRYYA 652

Query: 673  VQAKKMMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIA 732
             +A ++  +P  LPGP GE N L   GRGVF+CISPWNFP+AIF GQ+AAALA GNTV+A
Sbjct: 653  ARALELFDRPMALPGPCGEDNFLTYYGRGVFLCISPWNFPIAIFTGQIAAALAAGNTVVA 712

Query: 733  KPAEQTCLIGFRAVQLAHEAGIPKDVLQFLPGTGAVVGAKLTSDERIGGVCFTGSTTTAK 792
            KPAE T L     V+L H+AGIP  VL F+PG G+ +G  L  D RI GV FTGST TA+
Sbjct: 713  KPAEATSLTAAACVKLLHQAGIPGPVLNFVPGIGSEIGPLLLRDPRIAGVAFTGSTETAR 772

Query: 793  VINRALAGRDGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLY 852
             INR LA     I+PLIAETGGQNAM+ D+++  EQ+V D V SAF SAGQRCSALRVL+
Sbjct: 773  SINRQLA-EHADIVPLIAETGGQNAMIADTSAHKEQLVLDAVQSAFNSAGQRCSALRVLF 831

Query: 853  LQEDIAERVLDVLKGAMDELTLGNPGSVKTDVGPVIDAAAKANLNAHIDHIKQVGRLIHQ 912
            L  + A++++++L GAM +LT+G+PG   TD+GPVID  A   LNAH++ ++Q   ++ Q
Sbjct: 832  LPHETADKIIELLIGAMQQLTIGDPGHYATDIGPVIDRKALDKLNAHVEAMRQHAGILFQ 891

Query: 913  LSLPEGTENGHFVAPTAVEIDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLT 972
              LP    +G +  PT +EIDS+  LT+E FGPILH+VRY +  L++VIDDIN+TG+GLT
Sbjct: 892  SPLPPELPDGTYFPPTLIEIDSLAQLTEEVFGPILHIVRYSSNTLEQVIDDINATGYGLT 951

Query: 973  LGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAGGPHYLTRF 1032
            LGIHSR    A ++  +  VGN+YINRN IGA VGVQPFGG GLSGTGPKAGGP YL RF
Sbjct: 952  LGIHSRINATARKIQQQAKVGNLYINRNMIGATVGVQPFGGMGLSGTGPKAGGPDYLKRF 1011

Query: 1033 VTEKTRTNNITAIGGNATLLS 1053
              E+T T N  AIGGNA+LL+
Sbjct: 1012 AVEQTVTINTAAIGGNASLLN 1032


Lambda     K      H
   0.317    0.134    0.380 

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: 2330
Number of extensions: 91
Number of successful extensions: 8
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: 1058
Length of database: 1036
Length adjustment: 45
Effective length of query: 1013
Effective length of database: 991
Effective search space:  1003883
Effective search space used:  1003883
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

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

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

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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