GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natH in Pseudomonas fluorescens FW300-N2E2

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate Pf6N2E2_5404 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q8YPM7
         (381 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5404 Glutamate Aspartate
           transport system permease protein GltK (TC 3.A.1.3.4)
          Length = 365

 Score =  249 bits (636), Expect = 9e-71
 Identities = 147/379 (38%), Positives = 218/379 (57%), Gaps = 40/379 (10%)

Query: 4   LTWLRKNLFSTWYNSLLTVICSALSLWLVQGIIVWATTKAQWAVIQVNLRLFLVGRFPQT 63
           + W+R N+FS+W N+LLT+    L   +V  ++ WA   A W             R   T
Sbjct: 20  VAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDANWVGTT---------RADCT 70

Query: 64  EYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGLFAFIVGLLLILFTLDLSSRLWLLL 123
           +    W+   I    G    G +     L WR                 +DL+  +WL +
Sbjct: 71  KEGACWVF--IQQRFGQFMYGYY--PADLRWR-----------------VDLT--VWLAV 107

Query: 124 TAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILWLI--GGGFGLRPVSSNLWNGLLLT 181
             V   P F+  SR        LS  +L+ +PI  W +  GG FGL  V+++ W GL+LT
Sbjct: 108 IGVA--PLFI--SRFPRKAIYGLS--FLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLT 161

Query: 182 LLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILYIEIVRGVPLIGILFLAQVMLPLFF 241
           L++A + IV + P+G++LALGR SN+P +R   + +IE  RGVPLI +LF++ VMLPLF 
Sbjct: 162 LVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFL 221

Query: 242 AADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLP 301
              +  D++LRA+ G++LF +AY+AE VRGGLQA+ +GQ EAA A+GL  +  + L++LP
Sbjct: 222 PEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILP 281

Query: 302 QALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGLIY 361
           QAL+ VIP +V  FI LFKDTSL+ ++GL +L    +   A P+++G   E Y+F  L++
Sbjct: 282 QALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVF 341

Query: 362 WLFCYSMSLASRRLERQLN 380
           W+FC+ MS  S  LER+L+
Sbjct: 342 WIFCFGMSRYSMHLERKLD 360


Lambda     K      H
   0.332    0.145    0.452 

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: 502
Number of extensions: 24
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: 381
Length of database: 365
Length adjustment: 30
Effective length of query: 351
Effective length of database: 335
Effective search space:   117585
Effective search space used:   117585
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 bits)

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

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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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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