Alignments for a candidate for PA5503 in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for PA5503 in Jannaschia aquimarina GSW-M26

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate WP_084629946.1 jaqu_RS16675 ABC transporter ATP-binding protein

Query= TCDB::Q9HT70
         (335 letters)



>NCBI__GCF_000877395.1:WP_084629946.1
          Length = 612

 Score =  169 bits (427), Expect = 2e-46
 Identities = 94/242 (38%), Positives = 143/242 (59%), Gaps = 6/242 (2%)

Query: 8   HKTYRVAGREIPALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGE 67
           H+     GR + A +     ++ G+  G++G SG+GKST+ R + RL +P+ GR+L++G 
Sbjct: 365 HRGLLGGGRLVHAAKSVDFALRRGETLGIVGESGSGKSTVARCVMRLIDPTSGRVLLDGR 424

Query: 68  DVTALDAEGLRRFRQRVGMIFQ--HFNLLSSKTVADNIAM-PLRLAGGFSRAEVDARVSE 124
           D+  L    LR  R+ + ++FQ  + +L   + V  +I   P+    G  +AE  AR  E
Sbjct: 425 DIAGLSQGALRPVRRDIQVVFQDPYRSLNPRRNVGQSITEGPVNF--GTPQAEAMARAEE 482

Query: 125 LLARVGLS-DHARKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQL 183
           L+  VGL  D   ++P Q SGGQ+QR+ IARALA +P +L+ DEA SALD    A VL L
Sbjct: 483 LMRVVGLDPDALERFPHQFSGGQRQRIAIARALAMQPHVLIADEAVSALDVSVQAQVLDL 542

Query: 184 LAEINRELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVF 243
           L ++     L ++ ITH++ V  ++CD++ VM  G +VEQG  ADV+ +PQH  TR  + 
Sbjct: 543 LDDVRDRFDLAMLFITHDLRVAAQICDRILVMRQGEVVEQGPTADVYANPQHDYTRALLA 602

Query: 244 EA 245
            A
Sbjct: 603 AA 604



 Score =  135 bits (339), Expect = 4e-36
 Identities = 87/245 (35%), Positives = 129/245 (52%), Gaps = 11/245 (4%)

Query: 20  ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEE-----PSGGRILVEGEDVTALDA 74
           A++   L + AG+I  ++G SG+GKS     +  L++     P  GRI+++GED+  +  
Sbjct: 101 AVEDIDLAVAAGEIVCVVGESGSGKSVTAFTVMGLQDSRALKPVAGRIMMDGEDLLRVGR 160

Query: 75  EGLRRFR-QRVGMIFQH--FNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGL 131
             LR+ R +++ MIFQ     L     V D I   L +    S +    RV   +  VGL
Sbjct: 161 RRLRKLRGEKMSMIFQEPMTALNPVARVGDQIGEMLEIHTDLSASGRKTRVIAAMEDVGL 220

Query: 132 SDHA---RKYPAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEIN 188
            D A   R +P QLSGGQ+QR+ IA AL   P +L+ DE T+ALD  T A +L L+ +I 
Sbjct: 221 PDPASMYRAFPHQLSGGQRQRIMIAMALVLEPDLLIADEPTTALDVTTQAQILDLIKDIQ 280

Query: 189 RELKLTIVLITHEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAERV 248
               + ++ ITH+  V+  + D+V VM  G IVEQG    V   P+HP T+  +     +
Sbjct: 281 ARRGMGVLFITHDFGVVADIADRVVVMQHGRIVEQGLAEQVLRAPEHPYTKMLMEAVPSM 340

Query: 249 DEDER 253
              ER
Sbjct: 341 TPPER 345


Lambda     K      H
   0.322    0.138    0.393 

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: 572
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 335
Length of database: 612
Length adjustment: 33
Effective length of query: 302
Effective length of database: 579
Effective search space:   174858
Effective search space used:   174858
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 (21.9 bits)
S2: 51 (24.3 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)
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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