Alignments for a candidate for nagF in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagF in Pseudomonas litoralis 2SM5

Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate WP_090276478.1 BLU11_RS13265 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::BFirm:BPHYT_RS02740
         (854 letters)



>NCBI__GCF_900105005.1:WP_090276478.1
          Length = 755

 Score =  281 bits (718), Expect = 1e-79
 Identities = 191/572 (33%), Positives = 301/572 (52%), Gaps = 14/572 (2%)

Query: 284 AGETLAPNTLAGVCAAPGVAVGK-LVRWDDADIDP-PEKANGTSAAESRLLDKAIATVDA 341
           AGE +       V  APGVA+G+ +V    AD+   P+K      AE  L  KA+  V A
Sbjct: 169 AGEVIQDTRFDAVPGAPGVAIGRAVVMLPPADLKAVPDKEVKDIDAEIALYRKAVEAVHA 228

Query: 342 DLDTTVRDASQRGAVGEAGIFSVHRVLLEDPTLLDAARDLISLGKSAGFAWREAIRAQIA 401
           D+       + +    E  +F V+ ++L+D +L +     I  G+ A  A R+ I A +A
Sbjct: 229 DIKRLSAKLAAQLRPEELALFDVYLMMLDDSSLGNEIIAGIRQGQWAQGALRDVINAHVA 288

Query: 402 ILTNIEDALLAERAADLRDIEKRVLRALGYTSATARTLPEEAVLAAEEFTPSDLSTLDRS 461
               ++D  L ERAAD++D+ +R+L  L        T P + +L AEE TP+ L  + + 
Sbjct: 289 RFELMDDPYLQERAADIKDLGRRLLACLQEAGRQRLTFPRKTILVAEELTPAMLGEVPKD 348

Query: 462 RVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTEL 521
           R+  LV   G  +SH AILAR  GIP ++   D  +   +  +++V+   G +   P++ 
Sbjct: 349 RLVGLVSVLGSGSSHVAILARAMGIPTVMGAVDLPYLRMDKLELIVDGNAGEVYSNPSQ- 407

Query: 522 DVERARLERTRLADVREANR---RTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADS 578
             E  R  R  + +  E +    +   +  VT DG  + +  N     D   +++ GA+ 
Sbjct: 408 --ELRRHYRELIREEMELSHGLEKLRAEPCVTLDGHRVPLWVNTGLFADIARSLDRGAEG 465

Query: 579 VGLLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEP 638
           VGL RTE+ F+     P+  E + +Y+A ++A       +RTLDVG DK + Y  +  E 
Sbjct: 466 VGLYRTEVPFMILDRFPSEKEQQATYRAQLEAFHPLPVTMRTLDVGGDKALSYFPIK-ED 524

Query: 639 NPALGLRGIRLAQVRPDLLDDQLRGLL-AVQPLGAVRILLPMVTDVGEL---IRIRKRID 694
           NP LG RGIR+    P++   Q+R +L A + L  +RI+LPM++ V E+   + +  R  
Sbjct: 525 NPFLGWRGIRVTLDHPEIFLVQIRAMLKASEGLENLRIMLPMISSVNEVEEALHLIHRAH 584

Query: 695 EFARELGRTEPIE-VGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLA 753
               + G + P+  VGVMIEVP+A   A +LAQ  DFLS+GTNDLTQY LA+DR    +A
Sbjct: 585 GEVLDEGISVPMPPVGVMIEVPAAVYQARELAQRVDFLSVGTNDLTQYLLAVDRNNPRVA 644

Query: 754 AQADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVP 813
                LHPAVL+ +    +   + GK + VCG +AGDP A  LL+ +G   LS++  ++P
Sbjct: 645 DLYHSLHPAVLQALMLVARACREAGKPMSVCGEMAGDPAAAVLLLAMGCDVLSMNATNLP 704

Query: 814 GIKARVRNLDYQLCRQRAQDALALESAQAVRA 845
            +K  +R +     +    +AL+ ++A  V++
Sbjct: 705 RVKWLLRQIRLSDAQALLNEALSQDNAYLVQS 736


Lambda     K      H
   0.317    0.133    0.371 

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: 1243
Number of extensions: 50
Number of successful extensions: 6
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: 854
Length of database: 755
Length adjustment: 41
Effective length of query: 813
Effective length of database: 714
Effective search space:   580482
Effective search space used:   580482
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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)
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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 2024 update 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