Alignments for a candidate for N515DRAFT_2924 in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for N515DRAFT_2924 in Stenotrophomonas chelatiphaga DSM 21508

Align Basic amino acid/polyamine antiporter, APA family (characterized, see rationale)
to candidate WP_057508922.1 ABB28_RS12355 amino acid permease

Query= uniprot:A0A1I1Y8J0
         (492 letters)



>NCBI__GCF_001431535.1:WP_057508922.1
          Length = 491

 Score =  603 bits (1556), Expect = e-177
 Identities = 301/494 (60%), Positives = 375/494 (75%), Gaps = 10/494 (2%)

Query: 1   MLKNLFATTQISPASADLPG----GGAHGEATLKRALTARHLVLLGIGAIIGAGIFVITG 56
           MLK L     + PA     G    G   GEATLKR LTA+HL+LLGIGA+IGAGIFV+TG
Sbjct: 1   MLKALLRVKPVEPAGHVDAGEPIEGSLDGEATLKRTLTAKHLILLGIGAVIGAGIFVMTG 60

Query: 57  QAAAEHAGPAIVLSFVFAGIACALAALCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGW 116
           QAAA HAGPA+ LSFV AG+ACALA LCYAEFAAM+PVSGSAYSYSYATLGE +AWF+GW
Sbjct: 61  QAAAFHAGPAVTLSFVLAGLACALAGLCYAEFAAMMPVSGSAYSYSYATLGEGMAWFIGW 120

Query: 117 SLVLEYLFTVATVAAGWSGYFNKLLALISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMF 176
            LVLEYLF  A+VA  WS Y   LL+ ++  +   +  P  L++AP     G   A+G  
Sbjct: 121 CLVLEYLFASASVAVAWSAY---LLSFVTTTL--HLPFPDALSSAPIAWEGGQFIASGQL 175

Query: 177 INLPAVAIIAAITGLCYVGITQSAFVNSIIVAIKVTVILLFIAFATKYINPDNWHPFIPA 236
            NLPAV I+AA+TGL YVGI+QS FVN IIVAIKV+VI LFI F   +I+  NW PFIP 
Sbjct: 176 FNLPAVLIVAAVTGLLYVGISQSTFVNGIIVAIKVSVICLFIGFGASHIDTANWQPFIPE 235

Query: 237 SEGA-SKYGWAGVGRAAAIVFFSYIGFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYI 295
           + G   ++GW+GV RA +IVFF++IGFDAVSTAAGE K+PQR+MPIG++GSL +CTI+Y+
Sbjct: 236 NTGTFGEFGWSGVLRAGSIVFFAFIGFDAVSTAAGETKDPQRNMPIGLLGSLAICTIIYV 295

Query: 296 IVAGILTGIADFRLLGTPEPVSTALDNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRI 355
           IV  +LTG+  ++ LGT +PV+TAL+ YP L WL+  V IGA+ GLSSV+LVM+MGQ RI
Sbjct: 296 IVCLVLTGLLPYQQLGTAKPVATALEAYPQLAWLKTAVEIGAIAGLSSVVLVMMMGQTRI 355

Query: 356 FYSMARDGLIPAVFGRIHQKFRTPHVGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFA 415
            Y+++RDGL+P   G++H +F+TP+V T++VGV+AAAL G+  + VLGE+V+MGTLLAFA
Sbjct: 356 AYTISRDGLLPRFLGKVHARFKTPYVATIIVGVIAAALAGMMPLNVLGELVSMGTLLAFA 415

Query: 416 TVCIGVLVLRYTRPELPRAFRVPVPWIVCPLGALACMALFLQSFLEHWRWMLAWIAIGQA 475
           TVCIGVLVLRYTRPEL R FRVP+ W++CPLGALAC+ LF  +F EHW   + W  +G  
Sbjct: 416 TVCIGVLVLRYTRPELVRPFRVPMAWLICPLGALACLTLFAMAFREHWHLFVGWTVLGLL 475

Query: 476 IYFLYGYSHSKLRK 489
           IYF YG  +SKL K
Sbjct: 476 IYFGYGMRNSKLAK 489


Lambda     K      H
   0.328    0.141    0.441 

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: 877
Number of extensions: 42
Number of successful extensions: 3
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: 492
Length of database: 491
Length adjustment: 34
Effective length of query: 458
Effective length of database: 457
Effective search space:   209306
Effective search space used:   209306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

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

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Steps (tab-delimited)
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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 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