Alignments for a candidate for glpA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpA in Klebsiella michiganensis M5al

Align anaerobic glycerol-3-phosphate dehydrogenase subunit A (EC 1.1.5.3) (characterized)
to candidate BWI76_RS19965 BWI76_RS19965 sn-glycerol-3-phosphate dehydrogenase subunit A

Query= ecocyc::ANGLYC3PDEHYDROGSUBUNITA-MONOMER
         (542 letters)



>FitnessBrowser__Koxy:BWI76_RS19965
          Length = 540

 Score =  889 bits (2298), Expect = 0.0
 Identities = 438/536 (81%), Positives = 482/536 (89%)

Query: 5   DSQSSDVIIIGGGATGAGIARDCALRGLRVILVERHDIATGATGRNHGLLHSGARYAVTD 64
           DS+  DVIIIGGGATGAGIARDCALRGL+  LVER+DIATGATGRNHGLLHSGARYAVTD
Sbjct: 3   DSREYDVIIIGGGATGAGIARDCALRGLKAALVERYDIATGATGRNHGLLHSGARYAVTD 62

Query: 65  AESARECISENQILKRIARHCVEPTNGLFITLPEDDLSFQATFIRACEEAGISAEAIDPQ 124
           +ESARECISEN+IL+RIARHC+EPT+GLFITLPEDD ++Q TFI AC++AGI A+ + P 
Sbjct: 63  SESARECISENRILRRIARHCIEPTSGLFITLPEDDPAYQHTFITACQQAGIEAQPLTPA 122

Query: 125 QARIIEPAVNPALIGAVKVPDGTVDPFRLTAANMLDAKEHGAVILTAHEVTGLIREGATV 184
           +   +EPAVNPAL+GAV+VPDGTVDPFRLTAANMLDA+EHGA ILT  EVTGL+REG  V
Sbjct: 123 ETLRLEPAVNPALLGAVQVPDGTVDPFRLTAANMLDAREHGATILTGCEVTGLLREGDRV 182

Query: 185 CGVRVRNHLTGETQALHAPVVVNAAGIWGQHIAEYADLRIRMFPAKGSLLIMDHRINQHV 244
            GV + +    E  +L A VVVNAAGIWGQ IAEYADLRI MFPAKGSLLI+DHRIN+ V
Sbjct: 183 QGVALYDRQRREPLSLRAQVVVNAAGIWGQRIAEYADLRIAMFPAKGSLLILDHRINRQV 242

Query: 245 INRCRKPSDADILVPGDTISLIGTTSLRIDYNEIDDNRVTAEEVDILLREGEKLAPVMAK 304
           INRCRKP+DADILVPGDTISLIGTTS+ I Y+EIDDNRVTA EVD LLREGEKLAP+M +
Sbjct: 243 INRCRKPADADILVPGDTISLIGTTSMHIPYDEIDDNRVTAGEVDTLLREGEKLAPIMGR 302

Query: 305 TRILRAYSGVRPLVASDDDPSGRNVSRGIVLLDHAERDGLDGFITITGGKLMTYRLMAEW 364
           TRILRAYSGVRPLVASDDDPSGR+VSRGIVLLDHA+RDG++GFITITGGKLMTYRLMAEW
Sbjct: 303 TRILRAYSGVRPLVASDDDPSGRSVSRGIVLLDHAQRDGMEGFITITGGKLMTYRLMAEW 362

Query: 365 ATDAVCRKLGNTRPCTTADLALPGSQEPAEVTLRKVISLPAPLRGSAVYRHGDRTPAWLS 424
           ATDAVCRKLGNT PCTTAD  LPGSQEP E TLRK+I+LPA LRGSA+YRHGDRTPAWL 
Sbjct: 363 ATDAVCRKLGNTAPCTTADAPLPGSQEPTETTLRKIIALPASLRGSAIYRHGDRTPAWLG 422

Query: 425 EGRLHRSLVCECEAVTAGEVQYAVENLNVNSLLDLRRRTRVGMGTCQGELCACRAAGLLQ 484
           + R HRSLVCECEAVTAGEVQYAVENL V +LLDLRRRTRVGMGTCQGELCACRAAGLL 
Sbjct: 423 DSRQHRSLVCECEAVTAGEVQYAVENLAVKNLLDLRRRTRVGMGTCQGELCACRAAGLLA 482

Query: 485 RFNVTTSAQSIEQLSTFLNERWKGVQPIAWGDALRESEFTRWVYQGLCGLEKEQKD 540
           RFNVTTSA+S+ QLS FLNERWKGVQP+AWGDALRESEFTRWVY GLCGL+KE +D
Sbjct: 483 RFNVTTSARSLTQLSEFLNERWKGVQPVAWGDALRESEFTRWVYLGLCGLQKEHQD 538


Lambda     K      H
   0.320    0.136    0.403 

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: 1028
Number of extensions: 30
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: 542
Length of database: 540
Length adjustment: 35
Effective length of query: 507
Effective length of database: 505
Effective search space:   256035
Effective search space used:   256035
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: 52 (24.6 bits)

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

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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