Alignments for a candidate for put1 in Nitriliruptor alkaliphilus DSM 45188

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Nitriliruptor alkaliphilus DSM 45188

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_083442147.1 NITAL_RS10705 hypothetical protein

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>NCBI__GCF_000969705.1:WP_083442147.1
          Length = 1116

 Score =  313 bits (802), Expect = 6e-89
 Identities = 283/885 (31%), Positives = 400/885 (45%), Gaps = 98/885 (11%)

Query: 267  ETISEALANARKYEAEGFRYSYDMLGEAAMTEADAQRYLASYEQAINAIGQASRGRGIYE 326
            + ++  LA AR   A+G + + ++LGEA + E +A+R L   E+ ++ + +         
Sbjct: 115  DALAARLAGAR---ADGQQLNINLLGEAVLGEREARRRL---ERTLDLVARPDVDH---- 164

Query: 327  GPGISIKLSALHPRYSRAQHERVIGELYGRLKSLTLLARQYD--IGINIDAEEADRLEIS 384
               +S+K++ +  + +    E  +  +  RL+ L L A   D    +N+D EE   LE+S
Sbjct: 165  ---VSVKITGITAQLNPWAFEAELERIGDRLRRLYLAAAATDPPTFVNLDLEEHRDLELS 221

Query: 385  LDLLERLCFEPELAGWNGIGFVVQGYQKRCPFVIDYLIDLARRSRHR----LMIRLVKGA 440
            ++   RL  E  L      G V+Q Y       +  L+  A + R      + IRLVKGA
Sbjct: 222  VEAFTRLLDESALHQVEA-GIVLQAYLPDSVAALQRLMSWAAQRRASGGAPVRIRLVKGA 280

Query: 441  YWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARKLLS--VPDVIYPQFATHNAHTLAA 498
                E   A++ G    P Y  K  TD +Y      +L       +    A+HN   +A 
Sbjct: 281  NLAMERVEAELHGWPAAP-YPTKADTDANYKRLVDLVLDPGALGAVKVGIASHNLFDVAW 339

Query: 499  IYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGKFNRPCRIYAPVGTHETL---LA 555
               +A           + L GM  P     VG  A        R+Y PV   +     ++
Sbjct: 340  ALLLAEERGVADHVRVEMLQGMA-PGEAAAVGRRAG-----ELRLYTPVVARDDFDVAIS 393

Query: 556  YLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMHADEGALGLPHPRIAQPRTL 615
            YL RRL E  A  +F+        +L  L++DP     +      A+G  H    +PR  
Sbjct: 394  YLFRRLEETSAPENFLR-------ALPHLISDPSVFDREAQRFVTAVGRRHEVPTEPRRT 446

Query: 616  YGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLGTEAAAGEDV-NQPAPVRNP 674
                    A +D                  +E  +   L G  A A + V   PAP+R P
Sbjct: 447  QDRRSEEPAVLDRF---------------VNEPDTDPSLPGNRAWAEDLVATPPAPLRTP 491

Query: 675  SDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAAALERAAELMEAQMQSLMG 734
                        A +AE E  +   V A P W A  A  R   L   A  +  Q   L+ 
Sbjct: 492  ----------IPAEVAEAEGLVSDLVTAQPTWHARGAAGRREVLHAVAAELSRQRGELVR 541

Query: 735  IIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSD--THRPLGPVVCISPWNFPLAI 792
            ++V EAGKT   A  EV EA+DF RYYA +  E  ++D   H PLG V+   PWNFP+AI
Sbjct: 542  VMVHEAGKTVGEADPEVSEAIDFARYYAERAPELETADGLRHEPLGVVLVTPPWNFPVAI 601

Query: 793  FTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAVQLLPGRGETVGAALVG 852
              G V AALAAGN V+ KPA +T   A         AGVP   ++  P   + VG ALV 
Sbjct: 602  PAGGVLAALAAGNAVILKPAPETRRCAELVAEACWAAGVPEDVLRFFPCEDDEVGQALVS 661

Query: 853  DARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQNAMIVDSSALAEQVVGD 912
               +  ++ TG++E A+L +             VPL+AET G+NA+IV  +A  +  V D
Sbjct: 662  HPDLGAIVLTGASETAQLFR--------TWNPDVPLMAETSGKNALIVSPAADLDLAVAD 713

Query: 913  VVNSAFDSAGQRCSALRVLCLQEEVAD--RVLEMLKGAMDELTMGNPDRLSTDVGPVIDE 970
            +V SAF  AGQ+CSA  +     +VA+  R L+ L  A++ L +G    L+T VGPVI  
Sbjct: 714  LVRSAFGHAGQKCSAASLAICFGDVAEDPRFLDQLVDAVESLVVGPSTDLATTVGPVI-H 772

Query: 971  EARGNIVRHIDAMRAKGR---RVHQADPNGAL-SAACRNGTFVSPTLIELDSIEELQREV 1026
               G + R +  +    R      Q   +G L S   R G                  E 
Sbjct: 773  RPEGKLERALTRLEPGERWLVEPRQLSEDGRLWSPGVRLGVTAGSW--------THTTEW 824

Query: 1027 FGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEVGNLYVNRNIV 1086
            FGPVL +VR   A LD  +A  N TGYGLT GIH+  D  +E  + + +VGN YVNR+I 
Sbjct: 825  FGPVLGIVR--AADLDEAIAIQNATGYGLTGGIHSLDDREVERWLAKVQVGNAYVNRHIT 882

Query: 1087 GAVVGVQPFGGEGLSGTGP--KAGGPLYLHRLLSVC----PLDAV 1125
            GA+V  QPFGG   S  GP  KAGGP Y+ +L + C    P D V
Sbjct: 883  GAIVQRQPFGGWKRSSVGPGAKAGGPNYVAQLGTWCEERPPTDVV 927


Lambda     K      H
   0.318    0.133    0.383 

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: 3149
Number of extensions: 165
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: 1333
Length of database: 1116
Length adjustment: 47
Effective length of query: 1286
Effective length of database: 1069
Effective search space:  1374734
Effective search space used:  1374734
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: 59 (27.3 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